A study on seasonal variations in the abundance of Lesser Flamingo (Phoenicopterus minor) in relation to phytoplankton abundance in lake Manyara was conducted for a period of fourteen consecutive months (July 2007 to August 2008). The aim was to relate the temporal variability in the phytoplankton species abundance and diversity of the lake to the population size of the Lesser Flamingo. Lesser Flamingo population numbers were obtained from monthly ground surveys whereby the lake was subdivided into defined counting vantage points. Water samples for phytoplankton species composition and biomass analyses were taken to the University of Dar es Salaam for laboratory analysis. The flamingo population estimates ranged from 9319 in August 2007 to 640,850 in August 2008. The Lesser Flamingo populations showed that temporal fluctuations were related to the changes in the abundance and diversity of phytoplankton species. The occurrence of Arthrospira associated with the increase in the abundance of Lesser Flamingo. It was observed that changes in the Lesser Flamingo numbers were influenced by the changes in the abundance and availability of their preferred food. The results indicated that microalgae assemblage positively correlated with ammonium and nitrate which were also related to the abundance of lesser flamingo. The phytoplankton community was dominated by cyanobacteria particularly Arthrosipira fusiformis likely due to the high lake salinity and pH that limited the growth of other microalgae. Correlation analysis showed strong correlation between the Lesser Flamingo abundance with the concentration of nitrate and ammonium and between the number of Lesser Flamingo and the cyanobacterium Arthrospira.