The obligate symbiotic relationship between dinoflagellates, Symbiodinium spp. and reef building corals is re-established each host generation. The solitary coral Fungia scutaria Lamarck 1801 harbors a single algal strain, Symbiodinium ITS2 type Clf (homologous strain) during adulthood. Previous studies have shown that distinct algal ITS2 types in clade C correlate with F. scutaria-Symbiodinium specificity during the onset of symbiosis in the larval stage. The present study examined the early specificity events in the onset of symbiosis between F. scutaria larvae and Symbiodinium spp., by looking at the temporal and spatial infection dynamics of larvae challenged with different symbiont types. The results show that specificity at the onset of symbiosis was mediated by recognition events during the initial symbiont-host physical contact before phagocytosis, and by subsequent cellular events after the symbionts were incorporated into host cells. Moreover, homologous and heterologous Symbiodinium sp. strains did not exhibit the same pattern of localization within larvae. When larvae were infected with homologous symbionts (Clf), similar to 70% of the total acquired algae were found in the equatorial area of the larvae, between the oral and aboral ends, 21 h after inoculation. In contrast, no spatial difference in algal localization was observed in larvae infected with heterologous symbionts. This result provides evidence of functional differences among gastrodermal cells, during development of the larvae. The cells in the larval equator function as nutritive phagocytes, and also appear to function as a region of enhanced symbiont acquisition in F. scutaria