The dynamic geological and climatological history of Southeast Asia has spawned a complex array of ecosystems and 12 of the 37 cat species, making it the most felid-rich region in the world. To examine evolutionary histories of these poorly-known faunas, we compared phylogeography of six species (leopard cat Prionailurus bengalensis, fishing cat P. viverrinus, Asiatic golden cat Pardofelis temminckii, marbled cat P. marmorata, tiger Panthera tigris and leopard P. pardus) by sequencing over 5 kb of DNA each from 445 specimens at multiple loci of mtDNA, Y and X chromosomes. All species except the leopard displayed significant phylogenetic partitions between Indochina and Sundaland, with the central Thai-Malay Peninsula serving as the biogeographic boundary. Concordant mtDNA and nuclear DNA genealogies revealed deep Indochinese-Sundaic divergences around 2 MYA in both P. bengalensis and P. marmorata, which is comparable to some described interspecific distance in Felidae. The divergence coincided with serial sea-level rises during the late Pliocene and early Pleistocene, and was likely reinforced by repeated isolation events associated with environmental changes throughout the Pleistocene. Indochinese-Sundaic differentiations within P. tigris and P. temminckii were more recent at 72,000-108,000 y and 250,000-1,570,000 y ago respectively. Overall these results illuminate the unexpected, deep vicariance events in Southeast Asian felids and provide compelling evidence of species-level distinction between the Indochinese and Sundaic populations in the leopard cat and marbled cat. Broader sampling and further molecular and morphometric analyses of these species will be instrumental for better defining conservation units and effectively preserving biodiversity in Southeast Asia.This article is protected by copyright. All rights reserved.