Certain crop plants are susceptible to pathogens or unable to develop efficient microbial symbioses. These crops adversely impact soil biological quality with consequences on plant health and productivity of cropping systems. Chickpea is a rotational pulse crop with two types: kabuli and desi, and several cultivars. Cultivation of chickpea has inconsistent effects on soil microbial communities and subsequent wheat crops. I conducted field studies and used high throughput molecular analyses to explore the variations among chickpeas to identify cultivars developing fungal communities that are conducive to plant health and productivity. I also carried out greenhouse studies and used biochemical analyses to investigate the response of chickpea cultivars to arbuscular mycorrhizal (AM) fungi and non-AM fungal endophytes and identify the influence of root and root metabolites on the endophytic and pathogenic fungi. Cultivars and types of chickpeas and environmental conditions promoted different fungal communities in the root endosphere. Funneliformis and Claroideoglomus were the dominant AM fungal genera and Fusarium and Alternaria were the dominant non-AM fungal genera in the roots of chickpea. The roots of cultivars CDC Corrine, CDC Cory and CDC Anna hosted the most diverse fungal communities in contrast to CDC Alma and CDC Xena roots which hosted the least diverse communities. Plant response to AM and non-AM fungal endophytes varied with genotype and type of chickpea. The root symbiosis effectively promoted plant growth in CDC Cory, CDC Anna and CDC Frontier and stimulated nitrogen fixation in CDC Corrine. Cultivars of chickpea responded differently to dual inoculation of the AM and non-AM fungal endophytes. Co-inoculation with AM and non-AM fungal endophytes had additive effects on CDC Corrine, CDC Anna and CDC Cory but non-AM fungal endophytes reduced the positive effect of AM fungi in Amit and CDC Vanguard. Desi chickpea appeared to form more efficient symbioses with soil fungal resources than kabuli chickpea. Protein(s) up-regulated in the mycorrhizal roots of the desi chickpea CDC Anna suppressed the growth of the fungal endophytes Trichoderma harzianum and Geomyces vinaceus and of the pathogens Fusarium oxysporum and Rhizoctonia sp. The formation of AM symbiosis decreased the production of root bioactive metabolites soluble in 25% methanol. Some of the root metabolites stimulated the growth of Trichoderma harzianum and Geomyces vinaceus, and a few inhibited Rhizoctonia sp. and Fusarium oxysporum. A few metabolites with contrasting effects on the different fungal species were detected. The non-protein phytochemicals had selective effects on the endophytes and pathogens whereas the antifungal proteins of mycorrhizal roots were non-selective. Overall the study reveals a "genotype effect" of chickpea on the soil microbiota suggesting the possibility to improve the performance of this crop through the selection of genotypes improving the communities of root associated fungi, by associating and responding to beneficial fungi and repressing the pathogens.