Abstract
The abundance of many Caribbean corals has declined over the past few decades, yet now Porites astreoides is 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 coral Orbicella annularis on reefs ( P. astreoides have 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. astreoides colonies O. annularis lacks across‐reef genetic structure, has low relatedness within and among reefs, and does not produce asexual larvae. Small‐scale genetic structure and high relatedness in P. astreoides are 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 of P. astreoides . Monitoring on these reefs from 1987 indicates that Porites has increased in abundance while Orbicella has decreased in abundance. The success of Porites is due to greatly increased settlement and recruitment compared with Orbicella . Together these results indicate that high numbers of locally retained and successful genotypes might explain the relative success of Porites on shallow, present‐day reefs in the Caribbean.