This study investigated the effects of environmental conditionson the microbiological quality of the European Anchovy (Engraulisencrasicolus) and the Round Sardinella (Sardinellaaurita) caught along the coast of Accra and Tema, Ghana by artisanal fishermen. A total of approximately, 500 g each of fresh E. encrasicolusand S. auritawith individual weights between 1.15 to 36.56 g and total lengths between 4.9 to 16.0 cm were collected from Accra and Tema at sea immediately after capture, on landing at landing beach, and at local retail markets. Three separate microbiological analyses were conducted to assess the changes in their microbiological qualities. Samples were aseptically macerated and serially diluted, and the pour plate and spread plate methods were used to enumerate total heterotrophic bacteria, total coliform bacteria, yeast and moulds and Bacillus cereus colonies in the samples. The results showed an increase in microbial loads from harvest to market in both fish species collected from both Accra and Tema. There were counts of microorganisms at all stages of production, but samples obtained from retail markets recorded colony counts of total heterotrophic bacteria (> 1.0 x 106 cfu/g) and total coliforms (> 1.0 x 104 cfu/g) higher than both local and international standards. Counts of yeast and moulds, and Bacillus cereus were recorded for samples of E. encrasicolus and S. aurita from both Tema and Accra, but these counts were within accepted limits (< 1.0 x 104 cfu/g) for consumption. It was concluded that, samples of both E. encrasicolus and S. aurita obtained at the retail markets recorded higher counts of microorganisms and therefore were contaminated. Fish handling obviously contributed to the increased microbiological load after harvesting. Education of fishers is required to improve their hygienic practices and should be followed by regular hygiene inspections.