To investigate the molecular bases of postzygotic hybridization barriers in tuber-bearing Solanums, the wild species Solanum commersonii Dunal ex Poir. (cmm, 2n = 2x = 24, 1EBN) and Solanum acaule Bitter (acl, 2n = 4x = 48, 2EBN) were crossed in intra- and interspecific genotypic combinations, and the transcriptome of immature seeds was analyzed by using the cDNA-AFLP technique. From a total of 423 analyzed cDNA fragments, 107 (25.3%) were differentially regulated in the compatible (acl × acl and cmm × cmm) versus incompatible (acl × cmm) crosses. DNA sequence data were obtained from 21 fragments and RT-PCR analyses were carried out with five fragments to validate the cDNA-AFLP differential pattern. Sequence analysis suggested a possible role for the differentially expressed sequences in cytokinesis, cell cycle, secondary and hormonal metabolism, biodegradation, and transport. In situ hybridization experiments with fragments encoding an ubiquitin-fold modifier 1 precursor and a possible vesicle transport protein revealed expression of these genes in the embryo and endosperm. The results suggest that the collapse of the embryo and endosperm in incompatible crosses may be related to alterations in cell cycle and cytokinesis.