Abstract-The occurrence and biological nitrogen fixation rates of epiphytic and benthic diazotrophs were studied in seagrass meadows at sites with seaweed farms and at a control site without seaweed farms from two locations, Chwaka Bay and Jambiani, along the east coast of Zanzibar. Ten species of cyanobacteria were encountered and Lyngbya majuscula and Microcoleus sp. were dominant in Chwaka Bay and Jambiani respectively. Cyanobacterial occurrence was significantly higher in seagrass meadows without seaweed farms (P<0.02), but there was no significant difference (P>0.05) in biomass (chlorophyll a). Biomass averaged 2.96±0.73 and 3.10±1.24 µg Chl a cm -2 in seaweed farms and 3.46±1.72 µg Chl a cm -2 at Chwaka Bay and 3.14±1.31 µg Chl a cm -2 at Jambiani in transects without seaweed farms. Nitrogenase activity showed no significant differences between sites with and without seaweed farms, (P=0.66 Chwaka and 0.75 at Jambiani). Fixation rates in sites without seaweed farms averaged 35.8±39.9 (Chwaka Bay) and 13.1±12.7 (Jambiani) µmol of C 2 H 4 produced/m 2 /hr, while with seaweed farms averaged 22.6±22.5 and 12.8±14.9 µmol C 2 H 4 produced/m 2 /hr at the same sites. There were no significant differences in nutrient levels between locations, sites with and without seaweed farms, or between tidal levels except for nitrate, which was significantly higher (P=0.01) at Jambiani than at Chwaka Bay. It was concluded that diazotrophs contribute a significant amount of exogenous nitrogen to the seagrass ecosystem, but no significant differences could be found between sites with or without seaweed farms.