Water monitors (Varanus salvator macromaculatus) are large lizards that inhabit wetlands. However, populations seem to be declining due to habitat fragmentation resulting from urban development. To develop an effective strategic conservation plan, the genetic diversity and population structure of water monitors at Bang Kachao Peninsula, a rich urban ecosystem in Bangkok, were analyzed using mitochondrial (mt) D‐loop II sequences and microsatellite genotyping. Both genetic markers indicated a high degree of population‐level genetic diversity. The consistency of the star‐shaped haplotype network and results of neutrality tests strongly suggest the occurrence of a recent expansion in the population, possibly driven by anthropogenic urbanization. Subpopulations at Bang Kachao Peninsula are unlikely but gene flow between water monitors has occurred, which is suggestive of female‐based dispersal. The large population of water monitors at Bang Kachao Peninsula creates conflict with local residents. Long‐term population management through translocation has been conducted by captive management at Varanus Farm Kamphaeng Saen. The results of genetic monitoring indicate that the captive research population was soundly established. Comparison of allelic profiles between the two populations is necessary before translocation of water monitor groups from Bang Kachao Peninsula to Varanus Farm Kamphaeng Saen to reduce human‐wildlife conflict. This work is the first step toward establishment of long‐term ecological monitoring and an in situ/ex‐situ conservation program, which are part of attempts to promote biodiversity in Thailand, following scientific principles.

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.