The molecular genetic characteristics were evaluated, and the genetic effects of marker loci on heterosis of three traits (birth weight, BWT; average daily gain, ADG; and feed and meat ratio, FMR) were analysed in the experimental pig populations: Yorkshire (Y, n=34), Landrace (L, n=46) and Meishan (M, n=55); Yorkshire×Landrace (YL, n=32) and its reciprocal (LY, n=36), Yorkshire×Meishan (YM, n=82) and its reciprocal (MY, n=47), by 39 microsatellite markers selected from pig chromosomes SSC4, 6, 7, 8 and 13. The results indicated that observed alleles ranged from 2 to 6, average 4.13, observed heterozygosity varied from 0.39 (Y) to 0.58 (YM+MY) and average polymorphism information content (PIC) varied from 0.33 (Y) to 0.5 (YM). There were two loci (sw2155 and sw1037) at which the alleles were fixed in Y and L, and there were three loci (sw2409, sw2454 and sw1691) at which the alleles were fixed in M. The results from heterozygosity and kinship analysis revealed an intrinsic genetic relationship among the seven populations. Furthermore, the results on genetic effect analysis indicate that several marker loci had a significant effect on heterosis of the three traits in the two different F1 crossbred populations (P⩽0.01), for example s0161, swr1130 and sw1856 for BWT, sw1856 and swr2036 for ADG, and sw1302 and swr2036 for FMR. The significant marker loci implied a deep genetic relationship between molecular marker loci and heterosis.