We tested the importance of in situ microphytobenthos (MPB) and transported material (seagrass, seagrass epiphytic algae, mangroves, saltmarsh succulents and saltmarsh grass in adjacent habitats) as ultimate sources of carbon to fish caught over mudflats. We measured d13C values of these 6 autotrophs and 22 fish species in the subtropical waters of Moreton Bay, Queensland, Australia. All fish d13C values lay in the enriched half of the range for autotrophs. We modelled the distribution of feasible contributions of each autotroph to fishes, and then pooled the contributions for autotrophs with similar isotope values. Carbon from the suite of autotrophs having enriched isotope values (seagrass, epiphytes, saltmarsh grass) provided much of the carbon to fishes: 90-100% of carbon for 3 species, 70-90% for 13 species, and 50-70% for 5 species. For the one other species, the contribution of these autotrophs was lower (30-50%), and for this species the contribution of in situ MPB might be as much as about 50%. We could not, however, separate the MPB contribution from that of mangroves and saltmarsh succulents, which was also low for most species. Organic matter from seagrass meadows is clearly important at the base of food webs for fish on adjacent unvegetated mudflats. We are uncertain whether the apparent contribution of saltmarsh grass is real or a spurious result due to the similarity in isotope values of this autotroph and seagrass. This suite of fish caught over mudflats is supported by food webs relying predominantly on carbon from adjacent habitats and not in situ MPB.