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Lima bean ( Phaseolus lunatus L.) is composed of two major gene pools. The Andean gene pool gave rise to the Gran Lima cultigroup, and the Mesoamerican gene pool gave rise to the Papa and Sieva cultigroups. In the Yucatan Peninsula, Lima bean presents a great diversity of landraces that belong to the Mesoamerican gene pool. However, studies so far have not been able to determine whether the Papa and Sieva cultigroup germplasm resources managed by Maya farmers can be morphologically or genetically differentiated. In addition, the physiological seed quality traits of P. lunatus are still unknown. Therefore, the objectives of the study were: (1) To evaluate morphological differentiation of the Papa and Sieva cultigroups of Lima bean and (2) To evaluate the physiological seed quality based on standard germination and emergence of seedlings tests. Results showed two well-defined groups. Group A comprised landraces JMC1288, JMC1336, JMC1364 and JMC1271 belonging to the Sieva cultigroup; group B included landraces JMC1208, JMC1264, JMC1313 and JMC1337 belonging to the Papa cultigroup. The germination percentage was 84%, and rate was 15 seeds germinated d −1 . The percentage of seedling emergence was 86%, and seedling emergence rate was 14 emerged seedlings d −1 . Results confirmed the presence of the Papa and Sieva cultigroups in the Yucatan Peninsula. The landraces of Papa cultigroup produced seeds with the best physiological quality for use in breeding and conservation programmes.