Rhipicephalus microplus (Canestrini, 1888) is one of the species with medical and economic relevance that has been reported in the list of Cuban tick species. Some morphological characterizations about the R. microplus species in Cuba have been published; however, molecular studies are lacking. Molecular phylogenetic analyses have grouped R. annulatus, R. australis and three clades of R. microplus in a complex named R. microplus. The present study aimed to characterize two R. microplus tick isolates, established as colonies at the Cuban National Laboratory of Parasitology. Morphological characterization of adult specimens was carried out by using Scanning Electron Microscopy. The sequences of mitochondrial genes: 12S rRNA, 16S rRNA and the subunit I of cytochrome c oxidase (coxI) and one nuclear sequence: internal transcribed spacer 2 (its2) were used for phylogenetic analyses. The life cycle under laboratory conditions for both isolates was also characterized. Tick specimens of both colonies showed morphological characteristics comparable with those distinctive for the R. microplus species. Phylogenies based on mitochondrial gene sequences identified congruently the Cuban tick colonies within the clade A of R. microplus. The life cycle of both isolates under laboratory conditions lasted 65 ± 5 days and the reproductive performance of female ticks of each colony also were similar with approximately 2500 larvae obtained from fully engorged female ticks. This study constitutes the first molecular characterization of ticks from the R. microplus species in Cuba.