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Eld's deer ( Rucervus eldii ) with three recognised subspecies ( R. e. eldii, R. e. thamin,  and  R. e. siamensis ) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of  R. e. eldii  using 19 microsatellite markers. Our results showed that  R. e. siamensis  exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1–0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between  R. e. eldii  and  R. e. siamensis  occurred around 0.4 Mya (95% HPD 0.3–0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore,  R. e. eldii  exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7–10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld’s deer and other species of the genus  Rucervus,  we propose to classify Eld's deer ( Cervus eldii ) in the genus  Cervus , which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies.

Population genetics and evolutionary history of the endangered Eld’s deer (Rucervus eldii) with implications for planning species recovery