ABSTRACT: This study aimed at determining whether fine-scale molecular diversity of Symbiodinium corresponds to functional differences in host/symbiont specificity during the onset of symbiosis in cnidarian/alga mutualisms. Infection experimentswere conducted in aposymbiotic larvae of the scleractinian Fungia scutaria using known algal Internal Transcribed Spacer (ITS)-2 types within Clade C. Our results show that algal type is directly related to specificity during the onset ofsymbiosis in F. scutaria larvae. The 3 ITS symbiont types (C1f, C15 and C31) within the major Symbiodinium Clade C engaged differentially in symbiosis with coral larvae. The homologous symbiont (C1f), foundin adult F. scutaria from the field, showed a significantly better association with the host larvae than the other 2 heterologous symbionts (C15 extracted from Porites compressa, and C31 from Montipora capitata). Thisis the first evidence that fine-scale ITS diversity of Symbiodinium confers functionality in the symbiosis.