The microbial communities established in three laboratory-scale compost matrix biofilters fed with toluene were characterized. The biofilters were operated for 7 weeks at inlet concentrations of toluene ranging over 250-500 ppm with daily irrigation, using a nutrient solution containing variable concentrations of nitrogen, supplied as urea, and other inorganic salts. The indigenous microflora of the compost included toluene-degrading species, making inoculation unnecessary. The numerically predominant toluene-degrading strains were isolated from the most diluted positive wells of most-probable-number counts on mineral medium with toluene as sole carbon source and identified by rRNA 16S gene sequencing. On the basis of sequence similarity, all the isolated strains were assigned to the species Pseudomonas putida, although some variations were observed in their respective sequences. It is concluded that the mode of biofilter operation including a daily supply of non-carbon nutrients created an environment favoring the constant numerical predominance of this fast-growing toluene-degrading species.