The objective of this study was to identify the dominant bacterial flora linked to the hygiene of dried and smoked fish in different geographical locations and to determine the presence of pesticide residues on the processed fish. Fish species were listed and collected. The bacterial ecology of dried and smoked fish from the northern zone of Cameroon was probed using a molecular technique employing variable regions of 16S rDNA profiles generated by PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis). The bacterial species were obtained by sequencing the PCR-DGGE bands and the pesticide residues by Chromatography coupled with mass spectrometry (GC-MS / MS), tested on 11 fish samples. Fifty three percent of the fish were smoked. Three types of pesticides have been identified on the dried fish samples. Among them, there were Cypermethrin (15 to 3600 µg/kg), Chlorpyrifos (19 to 8800 µg/kg) and Profenophos (62 to 92 µg/kg). The analysis of 16S rDNA profile and DNA sequencing revealed the presence of 32 bacterial species grouped into 22 genera. Dried fish were the most contaminated. Species such as Vagococcus carniphilus, Kurthia gibsonii, Lysinibacillus endophyticus, Macrococcus caseolyticus and Bacillus atrophaeus were present in the samples from all the locations. On a general note, the fish samples are of poor microbiological and sanitary quality.