The Asian elephant (Elephas maximus), a keystone species, faces significant threats from habitat loss, poaching, and population fragmentation. Understanding the evolutionary history of its subspecies is essential for developing targeted conservation strategies and mitigating risks to their survival.This study introduces, for the first time, whole-genome sequencing (WGS) data from predominantly wild-origin Asian elephants housed in European zoos, covering the distribution range of Asian elephants. Our data aims to validate the Asian elephant subspecies designation and address ambiguities about their origin, particularly concerning Bornean and Sri Lankan elephants. Analysis reveals a clear population structure with relatively recent splits, delineating three distinct genetic clusters: Borneo, Sumatra, and Mainland, with Sri Lanka forming an additional group. Hypotheses on the origin of Bornean elephants—native dispersal or human introduction—are explored. Our data reflects the current Asian elephant subspecies designation. This study is estimating the divergence time between Bornean and Sumatra elephants, around 170,000 years ago. Their genome also exhibited severe bottlenecks as recently as 8 and 38 generations ago, further supporting hypotheses of introduction. The divergence of Sri Lankan elephant from the Mainland is estimated at 48,000 years ago, with Sri Lankan elephants predominantly clustering with those from Myanmar, possibly due to historical trade networks. Additionally, the Sumatra elephant is confirmed as a distinct subspecies. Furthermore, the study discusses genetic management strategies for ex-situ populations, emphasizing the importance of implementing cluster-specific conservation measures. Despite data constraints, recognizing Bornean elephants as a distinct subspecies, informs conservation strategies, and suggests avenues for further research.