Primary productivity by plants and algae is the fundamental source of energy in virtually all food webs. Furthermore, photosynthetic organisms are the sole source for ω-3 and ω-6 essential fatty acids (EFA) to upper trophic levels. Because animals cannot synthesize EFA, these molecules may be useful as trophic markers for tracking sources of primary production through food webs if different primary producer groups have different EFA signatures. We tested the hypothesis that different marine macrophyte groups have distinct fatty acid (FA) signatures by conducting a phylogenetic survey of 40 marine macrophytes (seaweeds and seagrasses) representing 36 families, 21 orders, and four phyla in the San Juan Archipelago, WA, USA. We used multivariate statistics to show that FA composition differed significantly (P < 0.001) among phyla, orders, and families using 44 FA and a subset of seven EFA (P < 0.001). A second analysis of published EFA data of 123 additional macrophytes confirmed that this pattern was robust on a global scale (P < 0.001). This phylogenetic differentiation of macrophyte taxa shows a clear relationship between macrophyte phylogeny and FA content and strongly suggests that FA signature analyses can offer a viable approach to clarifying fundamental questions about the contribution of different basal resources to food webs. Moreover, these results imply that taxa with commercially valuable EFA signatures will likely share such characteristics with other closely related taxa that have not yet been evaluated for FA content.