Genomic studies regularly uncover morphologically cryptic and sympatric genetic substructure within hard coral species (Order: Scleractinia). Some of these cryptic taxa have been shown to respond differently to the environment via bleaching responses. Cryptic taxa have also been found to segregate by habitat attributes such as depth and reef position in relation to lagoon-slope or prevailing winds. Yet often these general distinctions do not fully explain the distributions of cryptic taxa. Moreover, the environment at the level of the individual is highly variable within these coarse habitat characterisations. Here we implement a novel approach of using 3D structure-from-motion to extract a range of physical characteristics that define the microhabitat experienced by individual coral colonies within the genus Agaricia. We used these measures to describe the micro-niches of genetically distinct coral taxa to investigate whether cryptic taxa differ in niche usage. Incorporating details of the microhabitat into environmental analyses can improve our understanding of environment-genotype relations and yield insights on the maintenance of genetic distinctiveness and coexistence of closely related sympatric taxa. In the future, uncovering such patterns may help to disentangle the effects of the environment vs. genotype in bleaching responses as well as aid in restoration efforts when choosing where within the reef to source or outplant specific genotypes or species.