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Background  Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish,  Collichthys lucidus  plays a vital role in the structure and functioning of marine ecosystem processes.  C. lucidus  has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure.    Results  A total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8  C. lucidus  populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of  C. lucidus  have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses.    Conclusion  The high genetic differentiation of 8  C. lucidus  populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural  C. lucidus  populations. In conclusion, this study could help us determine how  C. lucidus  populations will respond to future ocean temperature rising.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08045-8.

Population genomics provides insights into the population structure and temperature-driven adaptation of Collichthys lucidus