Mitochondrial displacement loop (mt D-loop) sequence analyses have greatly improved assessments of genetic diversity, structure, and population dynamics of endangered species threatened by climate change and habitat loss. Tracking population haplotypes of these species using mitochondrial-based markers has opened new avenues for conservation genomics and biodiversity research. Recent studies have used mt D-loop sequences to assess the genetic diversity of the largest land mammal in Asia, the Asian elephant (Elephas maximus), whose populations are rapidly declining. Here, we review haplotype data from mt D-loop sequencing studies and highlight previous population-scale hypotheses pertaining to the origin and diverse genetic profiles of Asian elephants. Retrieving haplotype information from elephant populations can substantially improve estimations of different parameters relevant to their conservation and allow introgression/hybridization dissection of genetic variation to shed light on ongoing evolutionary processes.