Aspects of maternal-planula larval genetics in the monoecious scleractinian coral Stylophora pistillata (Red Sea, Eilat) were studied by amplified fragment length polymorphism (AFLP) methodology in two successive reproductive seasons. In total, 293 planulae and 10 adult colonies were analyzed. In June 2006, 147 planulae were collected from 10 shallow water colonies. In March, April and June 2007, 146 additional planulae were sampled from five of the ten 2006 sampled colonies. All AFLP products showed unalike band profiles indicating a fully sexual production pattern. We used 181 and 210 putative AFLP loci, of which the overall level of polymorphism in 2006 was 92 and 99 % in 2007 (respectively). Differences were also observed between 2006 and 2007 reproductive seasons in terms of total average gene diversity (0.191 vs. 0.247, respectively), suggesting fast turnover of sperm donor genotypes. In addition, increased numbers of potential sperm donor colonies in the vicinity of gravid females showed no impact on genetic differentiation levels in released larvae. UPGMA tree revealed clustering of maternal genotypes and their offspring, suggesting, as expected, high relatedness between planulae and their mothers. In addition, the average heterozygosity of each group of siblings was persistently lower than heterozygosity calculated for the respective maternal colony, suggesting the possibility of partial inbreeding. This trend of reduced genetic heterogeneity in Stylophora pistillata is an alarming sign for populations residing in the northern Red Sea coral reefs.