Sitting in her little house near Tarbes, in the French Pyrenees, Marie-Pierre Manet-Beauzac is talking about her ancestry.

For most people this would be agreeable, perhaps even pleasurable. For the 40-something mother-of-three, the story of her bloodline is marked with a unique sadness: because she belongs to an extraordinary tribe of hidden pariahs, repressed in France for a thousand years.

Marie-Pierre is a Cagot.

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If the word "Cagot" means nothing to you, that is not surprising. The history of the Cagot people is obscure; some assert it has been deliberately erased. Marie certainly believes that: "To talk about the Cagots is still a bad thing in the mountains. The French are ashamed of what they did to us, the Cagots are ashamed of what they were. That is why no one, these days, will confess they are of Cagot descent."

Except, uniquely, for Marie-Pierre herself. She is probably the only person in the world willing to admit she is of Cagot blood. But it took her many years to realise what that meant. "When I first had children, I wanted to know where they came from – which means where I came from. And so I started researching, I traced my family tree back through the generations – through many villages and towns in the Pyrenees.

"And that's when I noticed certain names and trades in my background, lots of humble carpenters, basket-makers, poor people, people who lived in the 'wrong' parts of town. Soon I realised I was a Cagot. Though many argue what that really means."

As Marie-Pierre avers, the truth about the Cagots is obscure. The people first emerge in documents around the 13th century. By then they are already regarded as an inferior caste, the "untouchables" of western France, or northern Spain. In medieval times the Cagots – also knows as Agotes, Gahets, Capets, Caqueux, etc – were divided from the general peasantry in several ways. They had their own urban districts: usually on the malarial side of the river. These dismal ghettoes were known as Cagoteries; traces of them can still be found in Pyrenean communities such as Campan or Hagetmau.

For hundreds of years, Cagots were treated as different and inferior. In the churches, they had to use their own doors (at least 60 Pyrenean churches still boast "Cagot" entrances); they had their own fonts; and they were given communion on the end of long wooden spoons. Marie-Pierre adds: "When a Cagot came into a town, they had to report their presence by shaking a rattle. Just like a leper, ringing his bell."

Daily Cagot life was likewise marked by apartheid. Cagots were forbidden to enter most trades or professions. They were forced, in effect, to be the drawers of water and hewers of wood. So they made barrels for wine and coffins for the dead. They also became expert carpenters: ironically they built many of the Pyrenean churches from which they were partly excluded.

Some of the other prohibitions on the Cagots were bizarre. They were not allowed to walk barefoot, like normal peasants, which gave rise to the legend that they had webbed toes. Cagots could not use the same baths as other people. They were not allowed to touch the parapets of bridges. When they went about, they had to wear a goose's foot conspicuously pinned to their clothes.

Marie-Pierre sighs. "The Cagots weren't even allowed to eat alongside non-Cagots, nor share their dishes. Some said the Cagots were psychotic, even cannibals." As for marriage between Cagots and non-Cagots, it was almost impossible. Nonetheless, love affairs across the divide did occur – there are poignant songs from the 16th and 17th centuries lamenting these tragic misalliances.

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On occasions, the bigotry was brutally enforced: in the early 18th century a prosperous Cagot in the Landes was caught using the font reserved for non-Cagots – his hand was chopped off and nailed to the church door. Another Cagot who dared to farm his fields (strictly verboten) had his feet pierced with hot iron spikes. "If there was any crime in a village," says Marie-Pierre, "the Cagot was usually blamed. Some were actually burned at the stake." Even in death, the discrimination persisted – the Cagots were buried in their own humble cemeteries; there is still one in Bentayou-Sérée, a tiny village north of Pau.

So where did the Cagots originate? And why did they suffer such bigotry?

Their provenance is opaque. That is partly because the Cagots themselves have disappeared from view. During the French Revolution, the laws against Cagots were formally abandoned – indeed many Cagots pillaged local archives and erased any record of their ancestry. After 1789, the Cagots slowly assimilated into the general populace; many may have even emigrated.

Nonetheless, there are historical accounts that afford an intriguing glimpse. Contemporary sources describe them as being short, dark and stocky. Confusingly, some others saw them as blonde and blue eyed. Francisque Michel's Histoire des races maudites (History of the cursed races, 1847), was one of the first studies. He found Cagots had "frizzy brown hair". He also found at least 10,000 Cagots still scattered across Gascony and Navarre, still suffering repression – nearly 70 years after the Cagot caste was "abolished".

Since Michel's pioneering work, various historians have tried to solve the Cagot mystery. One theory is that they were lepers, or contagious cretins. That would explain the rules against Cagots "touching" anything used by non-Cagots. However, this theory falls down on the many descriptions of the Cagots being perfectly healthy, even sturdy.

Another idea, as Marie-Pierre implies, is that the Cagots were slaves of the Goths who inundated France in the Dark Ages. From here, etymologists have deduced that "ca-got" comes from "cani Gothi" – "dogs of the Goths". But that idea fails to explain the many variants of the Cagot name, nor does it square with the geographical distribution. In fact, the Cagot name probably derives from "cack" or "caca", a term of abuse in itself.

Last year, a new theory emerged, propounded by the British writer Graham Robb in his book The Discovery of France. Robb suggests that the Cagots were originally a guild of skilled medieval woodworkers; in this light, the bigotry against them was commercial rivalry, which became fossilised and regimented over time.

So who is right? It's a confusing picture. But Marie-Pierre Manet-Beauzac, "the last Cagot in the world", has no doubts where she comes from: "I believe the Cagots are descendants of Moorish soldiers left over from the 8th century Muslim invasion of Spain and France. That's why some people called them 'Saracens'. I am quite dark, and my daughter Sylvia is the darkest in her class."

And her theory, of the Cagots being converted but still-distrusted Muslims, is supported by many French experts: because it neatly explains the religious disapproval of the Cagots. As for the geographical spread, that's probably linked to the St James pilgrim routes.

Marie-Pierre shows me a website where she is gathering information about Cagot life. She points to a list of villages associated with Les Agotes.

"Some like to say Cagots have disappeared. But this is not true. If you travel near Campan, for instance, you can still see the short, swarthy people descended from the Cagots. The 'pestiferous people'."

I ask Marie-Pierre if she will let me use a picture of Sylvia – and the rest of her children. She shakes her head. "I'm sorry but no. It is OK for me to admit where I come from. But if people knew about my children's background, it might be difficult for them."

She gazes out of the window, at the distant green Pyrenees. "In some places, the hatred lingers. Even now. The Cagots may be silent but I can still hear it."

Other vanishing peoples

The Aromanians/the Vlachs

Whilst they date back to the Roman colonisation and its people are spread across much of the Southern Balkans, their language, Aromanian, closely related to Romanian, is believed to be almost extinct. Evidence of the culture lives on; with festivals celebrated in Greece today.

The Rusyns

1.2 million Rusyns are estimated to be living in Europe with over half the population in Ukraine. Ethnically not recognized by the Ukraine due to Czechoslovakia's communist regime of the 1950's, a time when their Greek Catholic Church was also eradicated. The people are famed for their beautiful wooden churches and ethnic pride is on the rise in Slovakia where they also dwell.

The Sami

The indigenous population also known as Laps are spread across northern Sweden, Norway and Finland, the tribe have populated Scandinavia and Russia for at least 2,500 years. Strongly associated with reindeer herding which continues today, with just under 3,000 still practising in Norway.