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Abstract The abundance of many Caribbean corals has declined over the past few decades, yet nowPorites astreoidesis more common on many shallow reefs than in the 1980s and shows evidence of local adaptation. We compare the small‐scale (1–8000 m) genetic structure of this brooding species and the broadcasting coralOrbicella annularison reefs (<14 m depth) in St. John, US Virgin Islands, to examine how larval dispersal and asexual propagation contribute to the retention of genotypes within reefs. Populations ofP. astreoideshave genetic structure across reefs separated by a few 100 m, increased relatedness within reefs, and parthenogenetic larval propagation confirmed by parent–offspring genotyping. Within reefs,P. astreoidescolonies <1 m apart are more related, independent of clonal reproduction, than corals at greater distances. In contrast,O. annularislacks across‐reef genetic structure, has low relatedness within and among reefs, and does not produce asexual larvae. Small‐scale genetic structure and high relatedness inP. astreoidesare evident even without considering asexual propagation, but asexual reproduction enhances these differences. Neither species shows the genetic signature of inbreeding or reduced genotypic diversity despite the high within‐site relatedness ofP. astreoides. Monitoring on these reefs from 1987 indicates thatPoriteshas increased in abundance whileOrbicellahas decreased in abundance. The success ofPoritesis due to greatly increased settlement and recruitment compared withOrbicella. Together these results indicate that high numbers of locally retained and successful genotypes might explain the relative success ofPoriteson shallow, present‐day reefs in the Caribbean.