Skewed segregations are frequent events in segregating populations derived from different interspecific crosses in tomato. To determine a basis for skewed segregations in the progeny of the cross between Lycopersicon esculentum and L. pennellii , monogenic segregations of 16 isozyme loci were analyzed in an F 2 and two backcross populations of this cross. In the F 2 , nine loci mapping to chromosomes 1, 2, 4, 9, 10, and 12 exhibited skewed segregations and in all cases there was an excess of L. pennellii homozygotes. The genotypic frequencies at all but one locus were at Hardy–Weinberg equilibria. In the backcross populations, all except two loci exhibited normal Mendelian segregations. No postzygotic selection model could statistically or biologically explain the observed segregation patterns. A prezygotic selection model, assuming selective elimination of the male gametophytes during pollen function (i.e., from pollination to karyogamy) adequately explained the observed segregations in all three populations. The direction of the skewed segregations in the F 2 was consistent with that expected based on the effects of unilateral incompatibility reactions between the two species. In addition, the chromosomal locations of five of the nine markers that exhibited skewed segregations coincided with the locations of several known compatibility-related genes in tomato. Multigenic unilateral incompatibility reactions between L. esculentum pollen and the stigma or style of L. pennellii (or its hybrid derivatives) are suggested to be the major cause of the skewed segregations in the F 2 progeny of this cross.