We report on the occurrence and diversity of cyanobacteria in intertidal seagrass meadows at Ocean Road and Mjimwema, Dar es Salaam, Tanzania. Nutrients, temperature and salinity were measured as comparative environmental factors. A total of 19 different cyanobacteria taxa were encountered, out of which eight were found exclusively in Mjimwema, four exclusively in Ocean Road and seven were common to both sites. Oscillatoria, Lyngbya and Spirulina were the dominant cyanobacterial genera. Cyanobacterial coverage was higher in Mjimwema (31–100%) than in Ocean Road (0–60%). The levels of nutrients in tidal pool waters at Ocean Road ranged from 0.45–1.03 μmol NO3 -N/l, 0.19–0.27 μmol NO2 -N/l and 0.03–0.09 μmol PO4 -P/l. At Mjimwema the nutrient concentration ranges were 0.14–0.93 μmol NO3 -N/l, 0.20–0.30 μmol NO2 -N/l and 0.01-0.07 μmol PO4 -P/l . The nutrient levels were significantly higher at Ocean Road than at Mjimwema (P = 0.001 for nitrate and P = 0.025 for phosphate). There was no significant difference in nitrite levels between the study sites (P = 0.83). The low cyanobacterial diversity and coverage in Ocean Road is related to the high levels of nutrients and physical disturbance from sewage discharge and the harbour in the area.