Identifying genetic connectivity and discrete population boundaries is an important objective for man- agement of declining Caribbean reef-building corals. A double digest restriction-associated DNA sequencing pro- tocol was utilized to generate 321 single nucleotide poly- morphisms to estimate patterns of horizontal and vertical gene flow in the brooding Caribbean plate coral, Agaricia lamarcki. Individual colonies (n = 59) were sampled from eight locations throughout southwestern Puerto Rico from six shallow (* 10–20 m) and two mesophotic habitats (* 30–40 m). Descriptive summary statistics (Fixation index, FST), analysis of molecular variance, and analysis through landscape and ecological associations and dis- criminant analysis of principal components estimated high population connectivity with subtle subpopulation structure among all sampling localities.