The better understanding of the diazotrophic communities is an important topic to explore the possible applications of biological nitrogen fixation. Present work provides an outline on how to utilize the molecular tools to study the changes in the diazotrophs community structure in terrestrial ecosystem. Molecular methods help us to understand the ecology, significantly elevating our knowledge of this process in soil. The mRNA study for the investigation of nifH transcripts in soil will add an influential tool to analyze the activity of the diazotrophs in more detail. The knowledge gained will make it possible to focus for enhancing biological nitrogen fixation in the field, either through amendments, optimized soil management, or by inoculation with specifically engineered or selected microorganisms. However, such technology will also leads to descriptive control and monitoring of the effectiveness of such future applications.