The terrestrial biota of the Caribbean islands includes many lineages, some whose presence on the islands dates back some 35–40 million years ago, when land bridges are thought to have linked islands to continents, and others that have colonised more recently via dispersal. The New World spiny orb-weavers (Micrathena Sundevall, 1833) are a diverse group of mostly Neotropical spiders. Eight species have been described on the Greater Antilles islands: three widespread and five single island endemics. Here, using three molecular markers (16S rRNA, ITS-2 and COI) we provide a preliminary phylogenetic test of the taxonomy and biogeography of Caribbean Micrathena through the first molecular phylogeny of the genus. Our analyses support monophyly of the genus, but not that of Caribbean Micrathena with at least 3–4 colonisations from South America. We sampled six of the eight nominal Caribbean species (M. banksi, M. cubana, M. similis, M. forcipata, M. horrida, M. militaris), but demark eight divergent genetic lineages that all are single island endemics, and morphologically distinct. Thus a revision of the taxonomy of Caribbean Micrathena is needed. Our results function foremost to guide more thorough taxon sampling of Micrathena that enable more rigorous assessments of its diversity and biogeography in the Caribbean.