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Biomass and cover of Microcoleus lyngbyaceus (Kutzing) Crouan were monitored at inshore seagrass habitats in southwest Puerto Rico for 16 months. Substantial localized blooms with maximum cover of 100% and comprising >600g/m 2 were encountered. Abundance of Microcoleus (biomass and percent cover) were not significantly correlated with either water temperature or water column nitrogen (as nitrate and nitrite concentrations). M. lyngbyaceus has locally been implicated as being detrimental to the seagrass Thalassia testudinum Konig which is supported by circumstantial evidence. Thalassia cover declined in permanent quadrats that were strongly impacted with Microcoleus.