This study was performed to evaluate the meiotic behavior and fertility of four hybrids obtained from the crossing of Capsicum baccatum and its botanical forms with Capsicum chinense and Capsicum frutescens. We aimed to identify the causes of the low fertility in interspecific hybrids involving species from different gene pools of Capsicum. Hybrid flower buds were fixed in fixative solution and the slides were prepared using 1%-acetic carmine solution. Meiosis was observed in all phases and the main meiotic abnormality observed was the complete or partial lack of chromosome pairing, indicating that the species are either genetically distant or that some asynaptic gene was present in the hybrids. Meiotic index (MI), the frequency of unreduced gametes (type 2n), and pollen viability were estimated. MI and pollen viability of the hybrids were low. We concluded that due to the complete or partial lack of chromosome pairing, the species used in the hybrid combinations are genetically distant. We also noticed that the low-fertility hybrids are a consequence of the lack of chromosome homology between the two genomes involved. The hybrids were considered partially sterile since their pollen viability percentage was lower than 50%.