Introduction: several studies have investigated the relationship between the estrogen receptor (ER) gene polymorphisms and the efficacy of estrogen replacement therapy in postmenopausal osteoporosis. However, the association of ER polymorphisms with the effects of dietary phytoestrogens on bone metabolism has not yet been reported. This study explores the possibility that ER alpha subtype (ERα) gene polymorphisms are involved in the effects of dietary phytoestrogens on bone mineral density (BMD) in postmenopausal women. Methods: a total of 301 postmenopausal southern Chinese women were enrolled. Dietary phytoestrogen intake was evaluated using a food frequency questionnaire. ERα polymorphisms were examined with restriction fragment length polymorphism at the polymorphic PvuII and XbaI sites within intron 1. Dual-energy X-ray absorptiometry scans were performed to determine the BMD of the lumbar spine and hip. Results: the positive association of the lumbar spine BMD with dietary phytoestrogen intake was maintained only in groups with pp or xx genotypes (p < 0.05) and disappeared in groups with other genotypes. A positive association of the hip BMD with dietary phytoestrogen intake was observed only in the xx genotype group (p < 0.05). Conclusions: the association of the dietary phytoestrogen intake and BMD in southern Chinese postmenopausal women varied with ERα gene polymorphisms.