Illegal wildlife trade is a major threat to global biodiversity. Asian elephants (Elephas maximus) are highly valued by various cultures as religious symbols and tourist attractions, which has led to a high demand for captive elephants. Owing to the unviability of captive breeding programs, several captive elephant populations are maintained by illegally obtaining wild Asian elephants. Morbidity and mortality rates among captive populations are high, whereas reproduction is low. In this study, we examined the genetic diversity among elephants using microsatellite genotyping and mitochondrial D-loop sequences of three captive elephant populations. The study results showed very low nucleotide diversity D-loop sequences and high variations in microsatellite genotyping, with an extensive variation of the gene pool estimates from different populations. This suggests that the optimal male selection during breeding could aid in maintaining the genetic diversity among captive populations. Forward genetic simulation revealed a decreasing genetic diversity in the fixed state within 50 generations. However, largely different gene pools can be effectively used to infer original elephant sources; this would facilitate the development of an identification certificate integration with machine learning and image processing to prevent illegal legislation owing to registration fraud between wild and domestic elephants. Implementing the proposed approaches and recommendations would aid in the mitigation of the illegal capture and domestic trade of wild elephants in Thailand and contribute to the success of future conservation plans in the blueprint of sustainable development goals.