Fish is a very perishable foodstuff whose preservation requires a continuous cold chain. The study aims to evaluate the effect of the break in cold chain on the bacteriological quality of Scomber scombrus (Atlantic mackerel) and Trachurus trachurus (Horse mackerel). Thus, data were collected from June to December 2016 in South Benin. A total of 120 fish were divided in control (cold chain integrity) and experimental (3h, 6h and 12h of break in cold chain) batches in order to determine the microorganism loads by cold chain break duration. Total Mesophilic Aerobic Flora (TMAF) and Clostridium perfringens loads were significantly higher in chilled fish samples than in frozen fish (p<0.001). However, no significant difference was observed between the control and the experimental batches whatever the preservation method and the cold chain break duration (p>0.05) for the TMAF. No Clostridium perfringens was counted for the freezing. Similarly, Staphylococcus aureus were not counted, except in the refrigerated batch for 3 hours of cold chain break. The TMAF and Clostridium perfringens loads increased according to cold chain break duration. For the FMAT, the highest load was observed at 12 hours of break in cold chain. In the majority of cases, Enterobacterium load was higher in the experimental batches compared to control batches. No samples revealed the presence of total coliforms, fecal coliforms, Salmonella and Escherichia coli. The rigorous cold chain keeping throughout the preservation until consumption significantly prevents the proliferation of fish contamination flora.