[13] Phylogenetic evidence supports Crocodylus diverging from its closest recent relative, the extinct Voay of Madagascar, around 25 million years ago, near the Oligocene/Miocene boundary.

[12] Below is a cladogram based on a 2018 tip dating study by Lee & Yates simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data,[14] as revised by the 2021 Hekkala et al. paleogenomics study using DNA extracted from the extinct Voay.

Crocodylus mindorensis is considered to be the most severely threatened crocodile species in the world, listed as critically endangered by the IUCN.

In mainstream Filipino society, crocodiles are considered dangerous man-eaters and compared to corrupt government officials and law enforcers.

C. mindorensis was considered locally extinct in part of its former range in northern Luzon until a live specimen was caught in San Mariano, Isabela, in 1999.

That individual, nicknamed 'Isabela' by its captors, was given to the care of the Crocodile Rehabilitation Observance and Conservation until it was released in August 2007.

They also recorded that tropical fire ants, an invasive species, eat unhatched endangered bukarot eggs.

In Spanish colonial records, the two species were often differentiated as cocodrilo (for C. porosus) and caimán for (for C. mindorensis), but this distinction is not followed by English dictionaries and translations.

[26] In Mindanao and Palawan, they are known as nguso in Agusan Manobo; sapding in Mandaya; balangitao or dagorogan in Maranao; bungut in Batak; and bungot in Tagbanwa.

[26] In the pre-colonial anito beliefs throughout the Philippine islands, crocodiles (both C. mindorensis and C. porosus) were feared and revered, which played a key role in their survival up until modern times.

The Spanish recorded that rivers and lakes were filled with crocodiles, and people often lived and fished close to them, which alarmed most European observers.

Some communities put up small bamboo fences to keep crocodiles out from certain areas and people avoided provoking them, but in general, they didn't take many specific precautions against them.

Thus attacks by crocodiles were regarded with fatalistic attitudes, as being the fault of the victim for transgressing taboos, or as punishment by the spirits for breaking an oath.

The Spanish conquistador Miguel López de Legazpi records in 1571 that his treaties with Sulayman, Ache, and Lakandula of Manila and Tondo were sworn on the condition that they would die and be eaten by crocodiles if they break the agreements.

Crocodiles were also believed to also exist in a sort of parallel spirit world, often interpreted as an underwater village.

[26] Depictions of crocodiles were commonly carved into coffins or woven into funeral clothes to protect the spirit of the deceased.

Crocodile teeth were also commonly worn as agimat (amulets) for protection against disease and evil spirits.