The microbiology of three different yoghurt samples from Mile I Diobu area of Port Harcourt was evaluated weekly for three weeks using standard plate count and most probable number (MPN) technique. This was carried out by analyzing for total aerobic heterotropic bacteria, total coliform bacteria, Thermotolerant coliform bacteria and fungi. The total aerobic heterotrophic bacteria count ranged from 4.0 × 105 cfuml-1 to 1.13 × 106 cfuml-1 of yoghurt, the total coliform bacteria ranged from 11 to 140 coliform (MPN) 100ml-1 while the thermotolerant coliform bacteria ranged from 17 to 90 coliform (MPN) 100ml-1 . The fungal count ranged from 1.0 × 102 spore forming unit (sfu) ml-1 to 5.0 × 102 sfuml-1 . The results of the mean values of pH of the samples were Green field yoghurt (pH 7.0), Home victory yoghurt (pH 7.5), and Mary gold natural yoghurt (pH 5.0). Generally, the bacterial, fungal and thermotolerant coliform counts were highest in the Mary gold samples which had an acidic pH. This shows that the isolates are acidophiles. On the other hand, the bacterial and fungal counts were lowest in Green field samples with a neutral pH which however, recorded the highest total coliform count. While the total coliform and thermotolerant coliform counts were lowest in the Home victory yoghurt samples. Generally, the incidence (%) of bacteria was; Bacillus cereus (22.5%), Bifidobacterium sp (7.5%), Escherichia coli (7.5%), Lactobacillus acidophilus (15%), Lactobacillus bulgaricus (12.5%), Pseudomonas aeruginosa (15%), and Staphylococcus aureus (20.0%). Incidence of fungi was; Aspergillus niger (10%), Fusarium solani (15%), Mucor sp (20%), Penicillium italicum and Penicillium spp (35%), and Saccharomyces cerevisae (20%). Statistical analysis using ANOVA showed that there is no significant difference at P = 0.05 in the microbial counts and in the incidence of the bacterial isolates between the three yoghurt samples. The presence of these bacteria and fungi especially enteric organisms and indicators of faecal contamination such as E. coli and Enterobacter is of public health concern as they pose serious health hazards to the unsuspecting consumers.