The paradise fish (Macropodus opercularis) is naturally distributed in western Taiwan, but is rare now because of such factors as environment pollution & habitat loss. Conservation of this animal in Taiwan is becoming more urgent. Some closely related species, such as Chinese paradise fish (M. chinensis), are difficult to distinguish with morphological characters. We sequenced & compared the control region of mitochondrial DNA (mtDNA) to reveal the genetic distance & molecular phylogeny of paradise fish populations from different geographical regions: Taiwan, Singapore, & mainland China. The interspecific distance between M. opercularis (Taiwan, Singapore) & M. chinensis (Zhejiang, Jilin) is 0.1341 ±0.0124, much more highly divergent than the distance between the Taiwanese and Singaporean populations, or within the Chinese populations. Five haplotypes from 11 specimens of the Taiwanese native population have been identified from a 1034-bp-length of mtDNA. However, the lower haplotypic diversity (H = 0.68) indicates a decreasing population in Taiwan, in contrast with the M. chinensis (H = 0.89). In addition, the unique genotype in Miaoli & Taichung may imply their subdivision because of exotic input of fish from a different geographic region. Thus conservation work should focus on avoiding the random release of paradise fishes into the wild.