AbstractSiniperca undulataandS. obscura(Centrarchiformes: Sinipercidae) are small Chinese perches, living in creeks and streams in southern China. While they have sympatric distribution and occupy similar macrohabitat, their body sizes and ecological niches have many differences. Determining the genome sequences ofS. undulataandS. obscurawould provide us an essential data set for better understanding their genetic makeup and differences that may play important roles in their adaptation to different niches. We determined the genome sequences of bothS. undulataandS. obscurausing 10× genomics technology and the next-generation sequencing. The assembled genomes ofS. undulataandS. obscurawere 744 and 733 Mb, respectively. Gene family analysis revealed that there were no overlap betweenS. undulataandS. obscurain terms of rapid expanding and rapid contracting genes families, which were related to growth, immunity, and mobility. Positive selection analyses also cooperated that the function of selected genes involve growth, athletic ability, and immunity, which may explain the preference of different niches byS. undulataandS. obscura. Pairwise sequentially Markovian coalescent analyses for the two species suggested that populations of bothS. undulataandS. obscurashowed a rising trend between 90 and 70 Ka probably due to the mild environment during the last interglacial period. A stage of population shrinking occurred from 70 to 20 Ka, which was in with the Tali glacial period in eastern China (57–16 Ka).