To investigate the input of combined nitrogen by cyanobacteria in mangrove ecosystems and the seasonal fluctuation of this biological process, in situ nitrogen fixation activity was measured in day and night experiments carried out at Maruhubi mangrove ecosystem adjacent to Zanzibar town. Sampling was done for 12 months at two stations: Station I covering sandy sediments and Station II muddy sediments. Associated cyanobacteria genera were identified and environmental variables were measured throughout the study period. A total of 10 genera of cyanobacteria were encountered, two of which were the heterocystous cyanobacteria genera Anabaena and Rivularia and eight the non-heterocystous genera Aphanocapsa, Merismopedia, Lyngbya, Microcoleus, Oscillatoria, Phormidium, Schizothrix and Spirulina. At both stations N2 fixation during the night was significantly higher (P ≤ 0.05) than during the day. The average N2-fixation rates at stations I and II were 1.64 and 1.34 nmole N2/hr/m2 respectively, with no significant differences (P ≤ 0.05) observed between seasons at both stations, or between stations in the rainy season. There was no significant correlation (P ≤ 0.05) between nitrogen fixation and physical-chemical variables, except sediment temperature, which showed a significant direct relationship with N2 fixation rate at Station I only. The results suggest that in the investigated ecosystem cyanobacterial diversity and nitrogen fixation are high; and generally seasonal changes do not have a significant influence on nitrogen fixation. It is therefore concluded that cyanobacterial diversity and nitrogen fixation process may contribute in the promotion of primary productivity in the mangrove ecosystem adjacent to Zanzibar town.