Epiphytic foraminifera are important components of the seagrass-meadow biota. These foraminifera previously were categorized, based upon their ecological and feeding strategies, into four morphotypes that were subsequently modified to include a new morphotype for the symbiont-bearing foraminifera. We propose further modifications to increase the ecological resolution. Thus, the A* morphotype splits into leaf-encrusting forms (AF*) and rhizome encrusting taxa (AR*). Similarly, the symbiont-bearing morphotype has been separated into Large Miliolids (LM) that host a variety of algal symbionts, and Large Rotalids (LR) that exclusively host diatoms. B and C morphotypes remain as they were originally defined, whilst D* morphotype does not include symbiont-bearing taxa and represents opportunistic forms. To determine the trophic strategy of the epiphytic morphotypes, the cytoplasmic nitrogen and carbon stable-isotope signals from two localities of Mallorca (Sa Foradada and Sant Elm) and one from Madagascar were analysed. The most abundant morphotype reported in Mallorca localities was B (38% ± 4.3 in Sa Foradada and 45% ± 4.2 in Sant Elm), followed by AF* (34% ± 4.6 in Sa Foradada and 41% ± 1.0 in Sant Elm). In Madagascar, the most abundant morphotype is D* (45% ± 10), and symbiont-bearing morphotypes (LM and LR) were considerably more abundant than at the Mediterranean locations. Among all samples, the δ15N values ranged between 0.5 and 3‰; δ13C values varied between −18 and −0.9‰. An MDS statistical analysis showed that variability in the δ15N and δ13C isotopes is associated with differences among the morphotypes and likely reflects their feeding strategies. A SIMPER analysis of the isotopic composition revealed minimal differences within the sessile (AF* and AR*) and within the symbiont-bearing (LM and LR) morphotypes, indicating similar trophic strategies within each pair, largely based upon cyanobacteria as a food source. These foraminifera perform “farming” of (cyano)bacteria, fungi and diatoms, which constitute the essential components of their diet. The LM-LR morphotypes also receive organic carbon from their algal symbionts. The δ15N and δ13C values of the motile B and D* morphotypes are highly variable, indicative of diverse food sources, including cyanobacteria, fungi, microalgae and particulate organic matter (phytodetritus). The δ15N in the C morphotype are more enriched and δ13C more depleted (3‰ and −10‰, respectively) than in the sessile morphotypes. Consistent with observations of other epiphytic, sessile organisms, cyanobacteria seem to be a very important food source.