Abstract: We evaluated domesticated Capsicum pepper species from Brazil using classical and molecular cytogenetic techniques, and describe here for the first time their immunostaining patterns using anti-H4K5ac and anti-H3S10ph antibodies. All accessions showed 2n = 24 chromosomes with metacentric and submetacentric morphologies. CMA3 patterns ranged from four terminal bands in most accessions to 18 variable CMA++/DAPI- and CMA+/DAPI0 bands. Anti- H4K5ac signals were detected in the decondensed terminal euchromatin of most chromosome arms, indicating gene-rich open chromatin regions. Anti-H3S10ph signals were restricted to pericentromeric regions and were associated with sister chromatid cohesions and/or the condensation of all mitotic chromosomes. These karyological analyses constitute valuable diagnostic tools for identifying cultivated peppers, will be important to Capsicum breeding programs and will provide additional cytogenetic features that can be used for the conservation of capsicum genetic resources.