Molecular biology techniques provide valuable information in terms of microbial dynamic and evolution. DGGE analysis is one of the most popular methods, which has been used in bioprocess assessment. A novel procedure that combines common experimental measurements, DGGE and image analysis is presented as a new methodology for preliminary assessment. Inthis study, the methodology was applied as an example to the start up of a hydrogen bioreactor, in order to have a preliminary estimation of the actual concentration of the different microbial species. The obtained results are used for determining the kinetic parameter by using a simple mathematical model focusing on species dynamic.