The impact of pig manure treatment was studied on bacterial populations of 17 piggeries using cultural methods and 16S rRNA targeted PCR Single-Strand-Conformation-Polymorphism analysis (SSCP). While both methods are conceptually and technically very different and even if they did not target the same microbial populations, the data obtained followed the same trends. Simple anaerobic storage did not promote a strong microbial community shift or reduction of faecal indicator numeration. Aerobic treatment followed by anaerobic storage induced strong microbial community shifts and resulted in a reduction of between one to two logarithmic units of the numbers of E coli and enterococci. This was not sufficient to totally eliminate Salmonella and Listeria monocytogenes. The dominant microbial community of the raw manures appeared very stable with the strong dominance of a few species whereas SSCP profiles of treated manures showed a greater diversity of bacterial population. The possible utilisation of molecular typing methods like SSCP is discussed as a tool to monitor microbial communities' diversity and stability, as well as a tool to identify and track specific manure indicators.