AbstractSponges are well known to feed heterotrophically through suspension feeding, but their relationships with photosynthetic symbionts mean they also have the potential to utilise or release photosynthetically derived carbon. Here, we determined the nutritional mode of sponges that occurred seagrass meadows at two sites in the Wakatobi National Park (Hoga‐1 and 2), Indonesia from the near‐reef flat (d = 1.9 m), middle‐shore (d = 1.2 m) and high‐shore (d = 0.5 m) zones to assess the role they might play in nutrient fluxes. We measured photosynthetic pigment concentrations and in situ net primary production to dark respiration (P:R) ratios of eight sponge species representing 75%–100% of the total sponge assemblage biomass at the two sites. We found that six of eight sponge species were autotrophic, based on their instantaneous P:R ratios and estimated daily oxygen production/consumption. The proportion of autotrophic sponge biomass in the high and middle shore of the seagrass meadows ranged between 40% and 70%, and accounted for 98% and 81% of the biomass in the near‐flat zones. Our findings that many seagrass sponges are autotrophic challenges the general view that sponges are consumers of organic carbon from the water column.