One of the most important challenges in microbial ecology is to determine the ecological function of dominant microbial populations in their environment. In this paper we propose a generic method coupling fingerprinting and mathematical tools to achieve the functional assigning of bacteria detected in microbial consortia. This approach was tested on a nitrification bioprocess where two functions carried out by two different communities could be clearly distinguished. The mathematical theory of observers of dynamical systems has been used to design a dynamic estimator of the active biomass concentration of each functional community from the available measurements on nitrifying performance. Then, the combination of phylotypes obtained by fingerprinting that best approximated the estimated trajectories of each functional biomass was selected through a random optimization method. By this way, a nitritation or nitratation function was assigned to each phylotype detected in the ecosystem by means of functional molecular fingerprints. The results obtained by this approach were successfully compared with the information obtained from 16S rDNA identification. This original approach can be used on any biosystem involving n successive cascading bioreactions performed by n communities.