Partially sterile interspecific hybrids were obtained between C. annuum var. 'cerasiformis' and C. chinense var. 'mishme' (H1), and C. annuum var. 'cerasiformis' and C. baccatum var. 'pendulum' (H2). Morphologically the F1 hybrids were intermediate between the corresponding parents. Meiosis was irregular in the two F1 hybrids. Cytological analysis of the two F1 hybrids revealed that the genome of C. annuum differs from C. chinense by two translocations and some minor structural alterations and from C. baccatum by two translocations, a single inversion and some minor structural alterations. Isolation barriers such as hybrid inviability, weakness and hybrid breakdown in the H1 hybrid and, inaddition, desynapsis in the H2, were operative in these taxa. The differences between the present findings and those reported earlier on the two F1hybrids were attributed to differences in the genetic architecture of the taxa employed in hybridization.