Follicle-stimulating hormone (FSH) stimulates granulosa cell proliferation and controls the development and maturation of oocytes. In this study with Rex rabbit, there was exploration of the relationships between reproductive traits and SNPs and haplotypes of FSHβ, and tested whether FSHβ SNPs would segregate between two lines, using 70 females from the White line and 100 females from the Beaver line. Three SNPs (FSH2, FSH30, FSH31) in exon1 and exon3 of FSHβ were strongly associated with reproductive traits in the combined population. For FSH2, the GG variant was associated with greater (P < 0.05) values for total number born (TNB) and number born alive (NBA), compared to those with the TT variant. For FSH30, for the AA variant there was greater (P < 0.05) values for TNB and NBA than with the GG and AG variants. For FSH31, the GG variant was associated with greater (P < 0.05) values for TNB, litter weight at birth (LWB) and litter size at 21 days of age (LS21), than the AG variant, and with greater (P < 0.01) values for NBA than the AG variant. When analyzed separately, FSH2 SNP was associated with LW21 in the Beaver line (P < 0.05), whereas FSH30 and FSH31 SNPs were associated with TNB and NBA in the White line (P < 0.05). It is concluded that genetic variation in FSHβ gene is associated with reproductive traits in the Rex rabbit, therefore, the FSH2, FSH30 and FSH31 SNPs can be used as molecular markers in genetic selection of rabbits.