The circulating levels of β-carotene are modulated not only by sex, but also by autosomal gene variations and fruit intake. The aim of this study was to investigate the interactions between β-carotene metabolism-related gene single nucleotide polymorphisms (SNPs; genetic factors) and nutrient intake (environmental factors) relating to their effects on circulating β-carotene. The serum concentrations of β-carotene and the habitual food intake of 92 healthy Japanese adults were examined. All subjects were genotyped for three common SNPs: rs6564851 in the β-carotene 15,15′-oxygenase 1 (BCO1) gene, rs2278986 in the scavenger receptor class B member 1 (SCARB1) gene and rs362090 in the intestine-specific homeobox (ISX) gene. Univariate analysis revealed that the circulating β-carotene levels were significantly higher in rs6564851 GG homozygotes (p = 0.003). Additionally, the daily intake of β-cryptoxanthin was positively associated with the circulating β-carotene levels in female GG homozygotes of rs6564851 (p = 0.023), and the daily intake of α- and β-carotenes, and β-cryptoxanthin was significantly lower in female rs6564851 T allele carries than in female GG homozygotes (p = 0.009, 0.008, 0.009, respectively). The present study apparently indicates that higher circulating β-carotene levels in female rs6564851 GG homozygotes depend on carotenoid intake.