Introduction. The severe impact of papaya bacterial canker in the West Indies justified launching a program to transfer the genetic resistance/tolerance identified in local germplasm to good-quality cultivars. As a first step, a germplasm collection from the Caribbean was gathered and its morphological and genetic diversity assessed. Materials and methods. The total sample included 50 accessions from the Lesser Antilles, Cuba, Venezuela, Costa Rica and Hawaii. Morphological data from a subsample of 29 accessions were submitted to analysis of variance, principal component analysis and Neighbor-Joining cluster analysis. Nine isozyme systems were tested, and the corresponding data were processed for cluster analysis and genetic parameters, including the fixation index, diversity indices and heterozygosity. Results. Eighteen of the 47 Caribbean and Venezuelan accessions exhibited hermaphroditism. Venezuelan accessions displayed the widest morphological diversity, while those from Barbados were distinguished by fruit quality. Sexual type affected leaf and flower traits. Cluster analysis shows little morphological differentiation between origins, with the relative grouping of the accessions from Guadeloupe or Barbados. Only four isozyme systems were polymorphic, producing 34 distinct zymotypes, with a relatively high heterozygosity and a particular diversity in Venezuela, Guadeloupe and Barbados. Geographic structuration appears limited in the cluster analysis among individuals; however, it is clearer when considering the six best-represented populations, with one cluster representing Venezuela, Trinidad and Barbados, and one for Guadeloupe, Martinique and Grenada. Discussion. The low level of fixation is attributed to dioecy and to the low level of selection. The relative isolation of island populations has favored geographic differentiation, albeit limited. The differentiation between the good-quality germplasm from Barbados and the tolerant populations from Martinique and Guadeloupe encourages the development of a marker-assisted introgression scheme.