In this study bacterial populations were identified in the rumen of zebu cattle fed various diets and classified taxonomically with metagenomic sequencing of the 16S rRNA gene. Twenty-four (24) heifers were used in a completely randomized experimental design to test the effect of the diets. Treatment 1 consisted of range grass hay. Treatment 2 was composed of the hay diet augmented with sun-dried cassava leaves. Treatment 3 comprised hay plus sun-dried azolla. Treatments 4 to 6 were similar to treatments 1 to 3. but with a basal diet of Brachiaria Mulato II hay. Rumen liquor samples were collected from the heifers, from which a total of 192 DNA samples were amplified and the resulting 16S rRNA sequences were compared with those in the National Centre for Biotechnology Information BLAST database using MetagenAssist. Bioinformatics analyses indicated that 17 operational taxonomic units (OTUs) were present at phylum level, of which 43.3% were Firmicutes, 27.2% Bacteroidetes, 22.8% Proteobacteria and 1.7% Euryarchaeota. The remaining OTUs were Cyanobacteria (1.4%) and Chloroflexi (1%) with Actinobacteria, Verrucomicrobia, Spirochaetes, Tenericutes, Planctomycetes, Elusimicrobia, Lentisphaerae, Armatimonadetes, Fibrobacteres, Synergistetes and Arthropoda all below 1% of the organisms present. Time and diet both affected (P <0.05) the abundance of microbes, but not their diversity in the rumen. Thus, these diets could affect the performance of animals.