Pacific salmon (Oncorhynchus spp., Salmonidae) are exposed to environmental and anthropogenic stresses due to their wide geographic distribution and complex life history. We investigated the causal effects on return rates of Japanese chum salmon (O. keta, Salmonidae), focusing on the period of sharp decline since the early 2000s, using more than 40 years of fishery and hatchery release data and high-resolution sea surface temperature (SST) datasets along the Japanese coasts and SST along the Japanese chum salmon migration route. We examined the geographic distribution of chum salmon allele frequencies using published isoenzyme datasets and a single nucleotide polymorphism (SNP) dataset collected from the range, focusing on lactate dehydrogenase (LDH), growth hormone, gonadotropin-releasing hormone and mitochondrial DNA loci. The effect of SST increases or decreases varied depending on the life history stage of the chum salmon. Winter SST in overwintering areas had a positive effect on return rates, whereas summer SST in coastal areas had a negative effect. The spike in 2022 was driven by an increase in age 4 fish, and the shift in age structure towards younger age at maturity occurred in all areas, being consistent with recent studies throughout Alaska. Allele frequencies varied with geographical patterns, with those in Japan significantly different from the overall trend, and those involved in metabolism and growth were close to Alaskan populations. We hypothesise that relaxed selection in hatcheries has altered allele frequencies, resulting in better growth in the first and second winters, thereby promoting a younger age at maturity.