The new European regulation 178/2002 imposes the determination of the geographical origin in the traceability process of the foodstuffs at the moment of commercial transactions. In practice, it is difficult to determine with accuracy the geographical origin of foodstuffs. For this purpose, the total analysis of the bacterial communities in samples is used. In the present study the molecular technique using 16S rDNA profiles generated by PCR-DGGE was used in order to detect the variation in bacterial community structures of Tilapia fish from three different lakes of the north of Cameroon and the effect of the season and fish species on these bacteria profiles. The V3 region of bacterial rDNA from fish was amplified by PCR and was analyzed by DGGE. When the 16S rDNA profiles were analysed by multivariate analysis, distinct microbial communities were detected. The bands profiles obtained from different lakes were different and specific for each location and could be used as a bar code to certify the origin of the fish. The fish specie did not have an influence on microbial profiles of fish contrarily to the season.