It's hard to explain to someone who has never fished Australia's fresh waters the veneration the trout inspires. Anglers don't capture them to eat them: they pursue them for the pure enjoyment of the dance - and the trout is a more than worthy partner. I know this because I fish. Chasing rainbows - or, rather, rainbow trout, carefree cousin to the brown - was a happy boyhood pastime around the volcanic lakes of western Victoria. Nothing could make me happier than the glint of a silver torpedo bursting from the surface as the rod kicked and bowed. Somehow, I'd always just assumed they belonged there. Neil Hyatt dips a hand into a deep tub and lifts up a thumping female rainbow, the fish slightly dulled by the tranquilliser he's mixed into the water. He holds it carefully for an instant, feeling its weight in his hand, only to send it splashing into a pond behind him. He's been working with trout for more than a decade and knows his charges well. This one's not ready. "Another week or two away," he says. Today, Hyatt's job is to examine the brood fish at the Snobs Creek Fish Hatchery in Victoria's east. The fish farm is a collection of tin sheds and shallow ponds, each watched over by a small, newly installed robot- like head that "coughs" food pellets into the water. Hyatt selects another female and discovers her to be ripe. He runs his fingers down her belly and a cascade of tiny, bright-orange bubbles squirt into a bucket below. He gives her a gentle shake and again "milks" her. Each hen can surrender as many as 2000 eggs in a single stripping. "You just shake them down," he says. His colleague, David Ambrens, is waist-deep in a nearby pond, herding male trout - or jacks - into a corner to be netted. He hoists one out and, holding it suspended over the bucket of eggs, runs his fingers down the jack's body to harvest its milt, sending a jet of white seminal fluid into the same bucket.

This is how humans manage what nature alone cannot, breeding and exporting trout to every corner of the earth, including Australia's coolest watery reaches. It's become big business; in the lakes around Jindabyne in the Snowy Mountains, for instance, the NSW government puts the value of trout fishing to the local economy at $70 million in tourist dollars. You can also find trout in the Adelaide Hills of South Australia, the southern tip of Western Australia, and in lagoons such as Little Pine and Penstock in Tasmania. They are there because people like Hyatt and Ambrens put them there - all for the thrill of the "dance". After a few weeks spent in well-oxygenated water maintained at four to seven degrees, the Snobs Creek eggs hatch. The hatchlings, only a few millimetres in length, eat the egg remnants and are then carefully fed ground fish food. Over the next 12 months they are kept in tubs inside a shed and then moved into outdoor "races", long pools that meander down a gentle slope like a running track. Here, they grow to between 10 and 15 centimetres, each weighing about 20 grams. Then the fingerlings' journey begins. A pair of 10-tonne trucks, equipped with tanks and oxygen bottles, trundle back and forth across Victoria, from east to far west, covering as many as 88,000 kilometres - the equivalent of more than two trips around the entire coastline of the Australian mainland - in a bid to populate the state's waterways with the fish. When the creatures are released, local fishing clubs are happy to help, usually transporting their intended quarry straight to their pet angling spots. Almost 500,000 brown and rainbow trout were introduced last year in Victoria, while the NSW government claims to have "liberated" about three million trout and salmon over the same period. A fair few of them have been duly unliberated by former prime minister and keen fly fisherman Malcolm Fraser. Many years ago, when Fraser was a new member of parliament, a much older colleague grabbed a couple of cane rods and took him away from Canberra for the weekend. They drove south to Adaminaby and Eucumbene Dam. Fraser had been going through a difficult time ("When you have a rough week [in politics], it's always with your own party, not a political enemy," he says) but now, on his first fishing trip, he captured a trout of such size that, in all the intervening years, he's never been able to snare a larger one. He also found mental release. "If you're thinking about fishing, you can't think about politics," he says. Over the years, he has filled the dams on his Victorian property with trout.

"They are unpredictable," he says, "and fun and difficult to catch." He imagines the fish were brought to Australia because native fish were not particularly good sporting fish. This belief, though widespread, is probably mistaken. The real reason more likely had more to do with homesickness - and the preservation of an old European habit - than the qualities, or lack thereof, of antipodean species. James Arndell Youl, a grazier whose family moved to Tasmania in 1819, earned a knighthood after succeeding in his determined mission to introduce the first salmonids, as members of the trout and salmon family are collectively known, into Australia. It was no easy feat. His delicate cargo of ova had failed to survive passage through the tropics on several voyages. But in 1864, aboard a ship called the Norfolk, Youl's fish eggs finally survived a 94-day voyage lovingly packed in damp moss in the vessel's ice house. Fraser, who has fished a lot of waters, counts Australian, and particularly Tasmanian, trout fisheries as among the best in the world. "There are people who say we should get rid of trout in Victorian waters," he says. "I think that quite ludicrous." Fraser's is a curious blind spot, and a common one. Studies have shown that when trout move in, tiny native fish almost always move out. Many species of local galaxias - minnow-like fish named for the shimmering stars on their scales - only exist in ghettos now, corralled above waterfalls where trout cannot go. Scientists in Tasmania spent $25,000 logging 78 working days and 51 nights at one lake to save one of the last breeding grounds of the almost extinct Clarence galaxias after zealous anglers had introduced trout. (Finger-sized trout can be bought from private farms. Releasing them into public waters without a permit is prohibited, but authorities make no effort to track their final destination.) When bushfires in years past soured water with ash, killing all the fish, trout were quickly reintroduced. The big-mouthed invaders stake out prime territory, around tangled tree branches in a river or the sunken boulders of cool-running streams. Trout hatch earlier than native fish and then hungrily patrol waters where local fish spawn. "They are just really effective predators," explains Susan Lawler, head of La Trobe University's department of environmental management and ecology. "They'll eat anything that fits into their mouths."

The International Union for the Conservation of Nature, the standard bearer for animal protection, now ranks brown and rainbow trout in the top 100 of the world's worst invasive alien creatures. The spotted tree frog in northern Victoria and southern NSW is critically endangered because trout eat the tadpoles that local fish leave undisturbed. Rainbow trout also carry a fish smallpox that has cruelled numbers of native Macquarie perch. Scientists speak of "impact" - the effect of the trout on native habitat - but, in Australia, the reckoning is imperfect. No one carried clipboards down to the river banks to count populations of native fish in the time before the foreigners arrived and, in many areas, trout no longer coexist with local species. "This lack of precision is often used by supporters of the trout industry to infer that there is no hard evidence of trout impacts," one study concluded. Victoria's fish-release policy was savaged last year by an official, though largely ignored, audit of the state's fresh waterways that revealed a lack of "robust scientific information or reliable data". The authorities, it reported, have a "structured, timely and transparent approach" when consulting recreational fishing groups, but there is "limited or no engagement" with natural-resource managers or conservation groups. The tension is obvious: the same authority responsible for protecting native species is also charged with filling lakes, rivers and streams with trout. Yet Australia does have a contender to rival, or even surpass, the trout as a freshwater sport fish, if only it could be given the chance. The "bluenose", as it's often called, is considered by many anglers to be the fastest and strongest freshwater fish on the line. It's misnamed the "trout cod" for its speckles, but it's not related to the trout. It is, in fact, a relative of the Murray cod.

Once prolific - it's thought to have previously ranged throughout the waters of the Murray Darling basin - the bluenose is now under threat, having been chased, literally, from their territories by trout. By the 1970s, the only remaining self-sustaining population in Victoria could be found in a stretch of creek below Polly McQuinn's Weir near Strathbogie, Victoria. Only a few existed in NSW. Breeding programs and catch bans have since managed to pull the fish back from the brink of extinction in trout-free lowland rivers. In a few short generations, it seems, the trout has conquered the collective memory. As a young man in the 1920s, local angler Bert McKenzie recalled catching bluenose on fly, spinners and bait in central northern Victoria, often while fishing for trout. The native, he used to laugh, made a real mess of his trout tackle. "I was never so sick of a fish in all my life. I wanted him to get away but I also didn't want to lose him. Anyone who wants real sport, should go to trout cod water." McKenzie, from Ruffy in the Shire of Strathbogie, was no slouch. He knew the deep holes in the rivers, was secretary of the local fishing club, and understood what Australia had lost. Waters once famed for their bluenose - the Goulburn River, Acheron River, Rubicon River and Big River - have become trout domain. McKenzie died in the early 1980s but his story emerges thanks to painstaking efforts by Will Trueman, a biologist and native fish enthusiast. His 2011 book, True Tales of the Trout Cod, comprises nearly 600 pages of oral testimony on early fishing in Australia. Old-timers such as McKenzie relate how the trout "went up every creek, every pothole, they grew fantastic", and how the natives, as a result, "got real scarce". This oral history has added to the scientific evidence of the trout's impact - and to demands for authorities to protect and cultivate local species. Over the decades, state governments have slowly embraced natives and now breed and release them in great numbers. Murray cod and golden perch (or yellowbelly) are favourites, with more than 1.8 million released in Victoria's warmer waters - those above 20 degrees, where trout struggle to survive - in the past year. Another 25,000 bluenose have also found new homes in the Goulburn River and at Beechworth. The locals are more difficult fish to rear in captivity, demanding live food such as yabbies, grubs or other fish. So while more natives are entering Australia's waters than trout, they are typically much smaller in size.

The Victorian government, spurred into action by last year's audit, has begun a study of the effects of trout release on native populations and upgraded its database. Scientists have no doubt that native fish populations would recover in the better-quality streams if trout stocking was halted. In many areas, trout populations are not wholly self-sustaining; they need humans as an ally. Loading Eradicating trout completely might be near impossible, yet trout-proof fences can be built. Thin wire gill nets have been stretched across mountain lakes in California's Sierra Nevada to kill the rainbow trout that were once transplanted there for the enjoyment of anglers. In mountain creeks in Victoria and NSW - the locations have not been revealed - barriers have been erected to protect endangered local fish by preventing trout leaping into cooler shallow waters. Perhaps the process has already begun. It is possible that global warming will spoil many of the cool waters trout colonise. When the trout go, the bluenose and others like it will be there to reclaim their birthright.