Abstract The effects of heavy metals from industrial effluents on non-symbiotic nitrogen-fixing population were studied in a soil from an industrial area polluted for nearly 40 years. The work reported differences in the number of heterotrophic N 2 fixers between contaminated and a non-contaminated one, confirming the great sensitivity to metals of this group of soil bacteria. Quantitative analysis of the response to increased doses of mercury reveals that the percentage of mercury tolerants was higher for contaminated soil. However the limit of mercury tolerance of diazotrophic bacteria seemed to be identical for both soils (6 µg/ml). Forty mercury tolerant diazotrophic isolates were obtained and further characterized. 16S ribosomal DNA sequence analysis revealed that Gram negatives dominated in both soils, but some of the bacterial lineages could not be detected in contaminated soil (α and β- Proteobacteria and Bacteroidetes ). Among mercury tolerant diazotrophic bacteria, genus Pseudomonas (10 isolates) and Bacillus (10 isolates) were predominant.