An increase in prevalence of lifestyle related diseases becomes one of the main threats to human health in Asia-Pacific regions. Especially Pacific countries face the marked epidemic of obesity and related disorders. Understanding of the genetic basis for these diseases is awaited. We investigated frequencies of 106 single nucleotide polymorphisms (SNPs) in genes associated with lifestyle related diseases in 1,878 individuals from five Asia-Pacific countries including Japan, China, Mongolia, Thailand, and Palau. Population genetic analyses revealed that disease susceptible variants of SNPs in TRIB3, PTGS2, ADIPOR1, DGAT1, UCP2, FOXC2, and ESR1 were overrepresented in the Palau population in comparison with the Asian populations. These gene variants likely contribute to the high prevalence of obesity and related diseases in Pacific populations. The present results would be helpful in coping with the lifestyle related diseases and may provide a new insight into the human dispersal in Asia-Pacific regions.