Human skin color is highly heritable and one of the most variable phenotypic traits. However, the genetic causes and environmental selective pressures underlying this phenotypic variation have remained largely unknown. To investigate whether the pigmentation related-genes polymorphisms are associated with the geographic environmental variables. We selected randomly 795 healthy individuals from eight ethnic groups in nine provinces in China. Six single nucleotide polymorphisms (SNPs) of SLC45A2 and TYR were genotyped using Agena MassARRAY. The Chi-square test and Spearman correlation analysis were used to compare the frequency distribution of genotypes among different ethnic groups and evaluate the relationship between SNP genetic diversity and environmental variables, respectively. The results indicated that rs28777 and rs183671 (SLC45A2) and rs1042602 (TYR) genotype frequency distributions were significantly different between the Xinjiang-Uighur and other ethnic groups (P < 0.05). Spearman correlation analysis found that rs28777-A (r = - 0.090, P = 0.011), rs183671-G (r = - 0.105, P = 0.003), rs1042602-A (r = - 0.108, P = 0.002), rs1126809-A (r = - 0.151, P < 0.001) allele frequencies were negatively correlated with the longitude; rs183671-G (r = 0.151), rs1042602-A (r = 0.157) and rs1126809-A (r = 0.138) allele frequencies were positively associated with the latitude (P < 0.001); rs183671-G (r = 0.116, P = 0.001), rs1042602-A (r = 0.105, P = 0.003) and rs1126809-A (r = 0.070, P = 0.048) allele frequencies were positively correlated with the sunshine hours; rs183671-G (r = - 0.076, P = 0.033), rs1042602-A (r = - 0.079, P = 0.027) and rs1126809-A (r = - 0.076, P = 0.031) were negatively correlated with the annual average temperature. Our results confirmed the idea that environmental factors have been an important selective pressure upon pigmentation related gene polymorphisms.