Malayan tapir is the only extant Asiatic species in the family Tapiridae, is endangered and threatened by risk of inbreeding from population structure. To elucidate the demographic and evolutionary history of the tapirs in Southeast Asia (SEA), this study analysed whole genome data from 10 individuals for historical effective population size (Ne) inference using sequentially Markovian coalescence (i.e., PSMC, MSMC, MSMC2), folded site frequency spectrum, (i.e., Stairway Plot 2), and their hybrid SMC++. The results revealed that tapir Ne ranged 6,000–12,000 in the last glacial period but went down to < 2,000 in recent time. Genomic analysis and population split time analysis (PSMC and SMC++) supported a population divergence (Fst > 0.25) between the Sumatran and mainland SEA tapirs since at least 6 kya. Subsidence of Sundaland and rainforest reduction were the major drivers for Ne decline. The timing of population split corresponded well with the inundation of Straits of Malacca to present-day levels by rapidly raising sea-levels during 10–6 kya. Results of this study, as well as contemporary geographical isolation, supports the subspecies status of the Sumatran population. This will have implication to the ex-situ conservation practices that may have produced hybrids of the isolated populations.