Jonathan Young tromped over ivy-covered hills and fallen trees, and through poison oak, tangled brambles and spider webs in a forest of Monterey cypress on Monday morning before he finally came across what he believes is a coyote den site.

“It’s like a tunnel maze, perfect for puppies,” said Young, wildlife ecologist for the Presidio Trust, as he stood on a sandy area in front of what looked like an entrance hole amid a labyrinth of logs and brush in a remote area of San Francisco’s Presidio. There are “places for them to hide, but enough structure for them to also play.”

There was no sign of the seven puppies that Young said were born in April, but a single juvenile coyote could be seen in the distance watching as Young emerged from the thicket. The collared animal, born a year ago, scampered off when he was spotted.

Reports from frightened dog walkers are increasing as they have in each of the past three years when the Presidio’s coyotes have had puppies. The annual rite of spring inevitably means there could be conflicts with dogs as the breeding pair and their four children from last year diligently guard the den.

Young is urging dog walkers to leash their pets and leave the area if a coyote approaches. He said breeding coyotes care less about people but can be unusually aggressive with other canines.

“The (coyotes) in the Presidio are afraid of people, but when they see a dog their parental protective instinct overrides their fear of you,” Young said. “They are concerned about the dog and just getting him out of there.”

Coyotes have been known to advance on, growl at or surround dog walkers and their pets, a pattern of aggression that is natural for the wild canines during pupping season, which begins in the spring and continues through the summer. The situation could get more tense, Young said, as the pups in the newest litter reach six to eight weeks of age and begin traveling with the adults around the park.

The displays are frightening and never fail to prompt demands from the public for authorities to remove or exterminate the yipping canines. Young said that people who encounter a coyote should leash their dogs and turn and walk, but never run, away.

Coyotes are generally afraid of people, he said, and can usually be scared off by standing tall and acting aggressively or using hazing techniques — shouting, waving a stick, throwing a rock. If the coyote stands its ground, it is almost always guarding a den and simply wants you to leave, he said. They will, however, occasionally prey on small dogs and cats.

The Presidio Trust, which manages 80 percent of the Presidio in partnership with the National Park Service, has closed the Park Trail between Mountain Lake and the Golf Course General Store and has put up signs urging people to be aware of coyotes.

Coyotes, which are native to San Francisco, recently moved back into the city after being gone for the better part of a century. The first modern sightings were in 2002. Two years later, Golden Gate Bridge officials viewed video of a coyote dashing across the span from Marin County in the dead of night.

The trust has had a coyote management plan since 2004 and began a comprehensive study of urban coyote behavior and ecology in San Francisco in 2015 in response to rising encounters and stepped-up concerns.

Now Playing:

Ten Presidio coyotes have been trapped and fitted with collars that have built-in radio transmitters and GPS technology. Young said he believes other coyotes have come into the city from the Peninsula. Young said as many as 50 coyotes have left the Presidio, including one collared male that was run over and killed in 2016 on Highway 280 in Los Gatos. Several other dispersing coyotes have also been killed by cars, he said.

Coyotes have since been confirmed in Golden Gate Park, Twin Peaks, Glen Canyon and Park Merced and have been seen numerous times roaming the 47-square-mile city. Young said he believes there are breeding pairs in each location and between 25 and 50 coyotes in the city at any given time.

Young said the biggest problem is when people feed the animals, which causes them to lose their fear of humans and become aggressive. Lethal control is the only solution in that case.

Right now there is one breeding pair, their seven puppies and four juveniles from last year’s litter in the Presidio, and they mostly hang around the Presidio golf course. The Presidio’s alpha male is easily identifiable because he has a torn ear. The alpha female has a collar, but it recently malfunctioned, Young said.

The pair recently moved their den from the golf course to the forested area between the Presidio golf course and Young’s office at Fort Winfield Scott. He had given up on seeing the pups Monday when he suddenly spotted a single puppy gazing at him curiously as he checked a trail camera.

“We walked right by them!” he said after snapping a hazy photo of the puppy in exactly the spot he had walked by several times that morning.

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com Twitter: @pfimrite