The predominant coconut variety cultivated in the Dominican Republic is a local Tall, known as criollo. It was never characterized genetically. The Malayan Dwarf and its hybrid with the local Tall are also present. Thirteen accessions, representing nine localities, are planted in a collection at the Instituto Dominicano de Investigaciones Agropecuarias y Forestales (IDIAF). We explored genetic diversity in 114 individuals from this collection. The main aim was to detect possible relationship with resistant varieties to coconut lethal yellowing (LY) disease. Contrarily to what happened in other Caribbean countries, LY never became an epidemic in the Dominican Republic. Thirteen simple sequence repeats markers from a kit dedicated to coconut diversity were used. In addition to diversity parameters, we used Bayesian assignment tests and cluster analysis to determine its population structure and its relationship with other coconut populations. The criollo coconut proved to be a typical Indo-Atlantic variety and is probably highly susceptible to the usual LY pathogens. Local conditions and the nature of the local phytoplasma strain probably explain the particular epidemiology of LY in the Dominican Republic. As a crosspollinating variety, the criollo presents polymorphism within a population, but there is little if any variation among populations. The marker study confirmed the hybrid status of each member of two accessions and, thus, the reliability of the sampling.