Ecosystem engineers alter local community structure and ecosystem functioning, and these impacts can be magnified when engineer populations are genetically diverse. Introduced populations typically have lower genetic diversity, which in theory constrains the positive effect of genetic diversity on ecosystem functioning. We tested for genetic diversity-function relationships in the introduced red alga Gracilaria vermiculophylla. Within high-salinity mudflats of Atlantic estuaries of North America, dozens of G. vermiculophylla thalli are glued onto individual worm tubes by the polychaete Diopatra cuprea (Onuphidae). A field survey in one estuary showed that these algal patches represent clonal fragments of between 6 and 18 multi-locus microsatellite genotypes. Within-patch genotypic diversity correlated with G. vermiculophylla biomass and epibacterial density, but had little to no effect on invertebrate or epifloral abundances, nor invertebrate diversity. To experimentally confirm these variable effects, we outplanted monoclonal and polyclonal (8 genotypes) patches into the mid and low intertidal for 28 days in spring and summer. We detected no impacts of genotypic diversity on primary productivity in spring nor in the summer at the low intertidal, but net primary productivity increased 300%in polyclonal relative to monoclonal patches in the mid intertidal during the summer. Genotypic diversity had little to no effect on any metric of secondary productivity or diversity. We conclude that modest increases in genotypic diversity can increase productivity of an introduced ecosystem engineer, but these impacts vary temporally and spatially for reasons that remain unclear. We also conclude that positive effects of genotypic diversity on primary productivity may not necessarily translate into secondary productivity.