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Cytogenetic and pollen viability (PV) studies were performed in pepper accessions, Capsicum chinense and Capsicum baccatum. Irregularities such as laggard and univalent chromosomes, bridges, problems in the spindle fibers and cytomixis were observed, especially in C. baccatum which was the most unstable genotype. In the post-meiotic products, irregularities were observed, on average, at 20 % of the microspores in C. baccatum and 17 % in C. chinense. PV in C. baccatum was below 70 %, while in C. chinense, it was above 80 %. Meiotic irregularities in Capsicum, mainly in C. baccatum, considering the low PV estimated, were significant but not impeditive for fertilization.