ABSTRACT Understanding strategies of organisms that utilise multiple modes of reproduction presents a complex challenge for evolutionary biologists. The genus Platygyra , a common reef‐building coral with unclear reproductive boundaries among morphological species, illustrates these complexities. Here, we evaluate the contribution of different reproductive modes in the coral P. daedalea at Heron Island, on the southern Great Barrier Reef, during the less prominent phase of a split‐spawning event, enabling assessment of reproductive outcomes associated with low population densities. We tagged and sequenced eighteen coral colonies, representing varying degrees of spatial clustering, along a 130‐m stretch of shallow reef slope. During spawning, divers trapped eggs from monitored colonies in mesh containers, which were then released into the surrounding water. High levels of spawning asynchrony were observed, potentially indicating distinct genetic clusters within the putative species, resulting in low fertilisation success (1.5%). Notably, paternity assignments revealed all resulting embryos were self‐fertilised, with no cross‐fertilisation detected, suggesting that self‐fertilisation may serve as a reproductive assurance mechanism in Platygyra during these smaller spawning events. The adult population showed evidence of two genetically distinct subpopulations, along with spatial autocorrelation and inbreeding. This supports the existence of smaller breeding units within larger assemblages, density‐dependent population effects and localised recruitment, indicating that these populations may be more hierarchically structured than previously recognised. Given the lack of evidence for in situ outcrossed fertilisation in this natural coral population during a minor spawning event, it appears that P. daedalea may utilise atypical modes of reproduction at low densities as observed here and/or alternatively rely on higher‐density spawning events and favourable hydrodynamic features not captured in this study.