It's known for its deadly bite, but the Philippine crocodile – thought to be the rarest in the world – has a lot more to give than it gets credit for. An effort blending science and indigenous knowledge to protect the species is helping replenish ecosystems and livelihoods.

In the lush, humid forest of the Philippines' Northern Sierra Madre Natural Park, three men in shorts, T-shirts and headlamps shape themselves a path through the night's thick vegetation with long sticks. They're treading quietly, calf-deep into turbid waters, and shining their torches against the darkness whirlpooling around their feet. Then, they see it. Quickly, they snatch the slender baby crocodile straight out of the safety of its muddy pond. What they are doing is not hunting or harming the infant yet stoic creature – one of the rarest crocodile species on the planet – but rather saving it from the brink of extinction.

Throughout history, the Philippine crocodile – known to science as Crocodylus mindorensis – could be found all over the Filipino archipelago, crawling around marshes, splashing in ponds and creeks, and trailing across fast-paced rivers nestled in limestone formations across the dense forests.

Historical records show that the indigenous people of the Philippines likely feared the small reptilian predator – which they called buwaya (crocodile) and bukarot (Philippine crocodile) – yet revered, venerated and respected it, living in harmony with it. Crocodiles were a symbol of strength and power, and villagers, especially tribe chiefs and the reptiles were thought to share intimate spiritual bonds. Some ethnicities believed that their ancestors would reincarnate as crocodiles, guarding over them in the years to come. If they spotted one among the turbid waters, they'd call out to them "Nono", or grandfather.

Spear fisherfolk were known to ask the crocodiles for permission to pass through their stretches of water and share nature's bounty, according to Nestor Aliejo, a leader of the indigenous Agta community in Dunoy and Villa Miranda, in the northern Philippines. "The crocodile is not really that harmful, as long as you don't hurt them," says Aliejo.

It was likely when the Spanish colonisers of the 1560s set foot on the islands that the perception of the reptilians started shifting. Apart from getting their taxonomy wrong and not distinguishing the Philippine crocodile from the saltwater crocodiles also found in the archipelago, records show high-ranking colonial officers wrote in their letters that crocodiles were everywhere, and they were "very bloodthirsty and cruel". One church fresco from San Mariano depicts a saint saving his people by stomping on a crocodile. Historians from the 1700s described crocodiles as "monstrous caimans" who killed people, especially children. (While indigenous credence among some ethnicities was actually that crocodiles never randomly assaulted humans, but rather they acted as divine arbiters, pruning evil in society.)

Over time, the Philippine crocodile's habitat was gnawed away at consistently through agricultural and industrial development, urbanisation, mining, slash-and-burn agriculture, and, since the late 1900s, legal and illegal logging as the Philippines became one of the world's largest exporters of tropical hardwoods. The rise of aggressive overfishing techniques like electrofishing also posed a risk to the wildlife in rivers.

The buwaya became indiscriminately persecuted: they were hunted out of fear of their attacks, for fun, as well as for the trade of their meat and precious skin. Their numbers plummeted. Estimates suggest that more than 80% of all of the archipelago's crocodiles have been killed in the past century – going from around 10,000 crocodiles (although this is hard to verify) to just 100 in the wild by the early 1990s – leaving small and rare pockets of populations in secluded inland freshwater habitats.

By the 2000s, all scientists could find was 20 crocodiles split among three interconnected river systemsin the Sierra Madre Mountains in north-eastern Luzon, a fragment of population in the small island of Dalupiri, and a likely larger population on the island of Mindanao. The latter, though, has been difficult to survey given the socio-political unrest in the area and there being armed groups in the marsh.

As a result, the Philippine crocodile was........

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