Technical Abstract: Many angiosperms have developed mechanisms to prevent self pollination and inbreeding. The most wide spread system of self incompatibility (SI) is gametophytic, where pollen tube growth is inhibited in the style by the action of a single locus (S-locus). Similar inhibition of pollen tube growth can also be observed in interspecific crosses, where successful pollinations occur in only one direction, termed unilateral incompatibility. We observed unilateral incompatibility in crosses between Solanum pinnatisectum and S. cardiophyllum and progenies were generated only when S. pinnatisectum was the staminate parent. Segregations in the BC1 family to S. cardiophyllum revealed two independent putative loci controlling unilateral incompatibility, with both putative loci inherited independently of the S-locus. However, segregation ratios in the second backcross family to S. pinnatisectum did not agree with those observed in the first family. Segregation disparity between the two families may be due to distorted transfer of specific alleles or the presence of different mechanisms controlling pistil and pollen recognition systems in these two species.