Ammonium (NH3) is an important nitrogen (N) source for plants and microorganisms. Bacteria convert N2 to NH3 by nitrogenase complex in nitrogen fixation process and this NH3 is assimilated and not released. However, there are some reports that N fixation in some mutant bacteria may lead to NH3 secretion. In this study wild strains producers of NH3 through N fixation without use of any mutant, were investigated as there were few reports about them. So, NH3 production in different N fixing bacteria like Paenibacillus, Rhizobium, Azotobacter, Agrobacterium and Klebsiella oxytoca, isolated from soil and plant roots of alfalfa (Medicago sativa), lentil (Lens culinaris), bean (Phaseolus luntus), pea (Pisum sativum), wheat (Triticum aestivum) and rice (Oryza sativa) was analyzed. NH3 production was assayed with Nessler reagent from bacteria cultured in two nitrogen-free medium (with two different carbon source including sucrose and mannitol) for one week. In the next stage, three strains of Paenibacillus (E, H, SH) with the highest NH3 production were selected and by means of an innovative system, production of NH3 in three different experiments (dry biomass of bacteria without any medium, in broth medium and wet biomass of bacteria located on slant medium) was assayed until production approached none (7 week). In the last stage, NH3 production by these bacteria was compared with non-nitrogen fixing bacteria during the ammonification process. Results show that from the 35 different isolated strains, only Paenibacillus strains were able to produce NH3 during the process of N fixation and accordingly seven strains of Paenibacillus were isolated (14.2 mM at the highest). The results indicated that dry biomass of E strain of Paenibacillus produced the highest amount of NH3 in the first week (22 mM). Paenibacillus produced greater amount of NH3 and for a longer time in comparison with ammonifynig bacteria. This is a novel way for the production of free ammonium.