In developing countries, advanced aquaculture techniques are still at the embryonic stage. This study was carried out from January to December 2021 in the ponds of the West Cameroon Region and at the Ichthyology and Applied Hydrobiology Research Unit of the University of Dschang with the aim of contributing to a better understanding of species richness and distribution of phytoplankton populations in fertilised ponds. For this purpose, a total of fifteen (15) ponds including 03 in Bamendou (fertilised with cow dung), four in Batié (two fertilised with pig manure and two with wheat bran), one in Dschang (fertilised with chicken manure), four in Fokoué (two fertilised with pig manure and two unfertilised), and three in Foumbot (fertilised with cow dung), were assessed. These ponds were chosen based on the availability of fish farmers and the type of fertiliser administered. Together with water physicochemical properties measurement, phytoplankton sampling was done between 6 a.m. and 8 a.m. on a monthly basis. The results showed that phytoplankton species and genera richness was higher in unfertilised ponds in Fokoué ponds and in animal feed enriched ponds in Batié, respectively. However, the highest family richness was obtained in Dschang receiving chicken manure with a percentage of 88.8% of the total family richness. The species Microcystis aeroginosa exhibited the highest species frequency (57%) out of all the species recorded in the ponds of Batié fertilised with pig manure. The lowest Shannon-Weaver diversity indices and Piélou evenness indices were recorded in the Fokoué ponds independent of the type of fertiliser, and in the Dschang ponds receiving chicken manure. The outputs of this work are better proposals for the production of phytophagous or bulldozer fish, such as carp, in relation to the site and the type of fertilisers in the Western highlands agroecological zone of Cameroon in particular and the world in general.