Locally-produced extracts of leaves and seed kernels of the neem tree, Azadirachta indica, have been successfully used as a pesticide in crop production areas of Mali. However, research has shown neem extract also acts as an antimicrobial agent and so studies aimed at examining how neem extract effects soil microbial community structure and function become necessary to fully appreciate ramifications of neem use in the environment. If neem extract affects soil microbial communities, soil catabolic function may also be affected, which in turn may affect future crop yield. Microbial communities in soil have a large impact on overall soil health oil due to their production of secondary metabolites, nutrient recycling and decomposition. Therefore, it was critical to monitor changes in the microbial community in soil exposed to neem extract. Soil samples were obtained from on-farm, IPM Collaborative Research Support Program (CRSP) research sites during a USDA Higher Education Challenge Grant externship in Mali (March 2004). We are currently optimizing molecular approaches to this problem, where PCR amplification of 16S and 18S rDNA is being used in conjunction with denaturing gradient gel electrophoresis (DGGE) to temporally track effects of neem extract (commercial and Malian village-produced neem kernel extract) on soil microbial populations. Near full-length clone libraries are also under construction, and we are exploring the use of a neem extract agar to facilitate cultivation of microorganisms capable of utilizing nutrients contained in the extract as well as are resistant to antimicrobials that are thought to be contained in the extract.