Despite being structurally limited due to their latitudinal distribution and local climatic conditions, mangroves of the southwest Gulf of California present productivity and carbon storage rates similar or higher than that of tropical mangroves. Despite the importance of their contribution to marine and atmospheric dynamics, few studies exist focused on food web structures in such ecosystems. In order to analyze trophic structure and dynamics of a mangrove system in the Gulf of California, the isotopic composition, trophic position, isotopic niche, and trophic pathways were studied using the statistical packages TrophicPosition (TP), SIBER, and Simmr. Isotopic values of C and N were obtained for 244 samples of carbon sources and invertebrate consumers which were classified into six trophic guilds. The δ13C values of carbon sources varied from −30.7 (Rhizophora mangle) to −15.6‰ (Caulerpa sertularioides) and for consumers varied from −22.3‰ (Aratus sp) to −13.2 (Callinectes arcuatus). Herbivores generally had depleted 13C values related to those of the other trophic guilds. The macroinvertebrate communities' mean TP values (2.6: 2.0–3.5) indicate a composition of primary and secondary consumers, exhibiting a clear separation between trophic guilds. Isotopic niche width (TA) of the community (14.1) suggests niche segregation, specially between herbivores and deposit feeders. Those trophic guilds are the first consumers and intermediaries for two distinct trophic pathways, one derived from detritus and mangroves and the other from microphytobenthos (MPB). Three groups of primary sources were identified contributing >70% of carbon, representing the primary base of several trophic pathways that sustain different consumer guilds: (1) mangrove-detritus, herbivorous crabs, (2) MPB-Sedimentary organic carbon, supporting mainly deposit feeders and filter feeders, and (3) Seston-MPB, supporting mainly omnivorous shrimp. Overall, the identified pathways potentially sustain fish communities, which due to their movement export energy from mangroves to coastal food webs.