We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea. This has been accomplished using culture-dependent and independent approaches to generate over 1,200 draft whole-genome assemblies at the level of bacterial populations, as well as 17 finished-quality genomes for a subset of strains representing the full, observed geographic and phylogenetic diversity of chickpea’s symbionts, using the Pacific Biosciences platform. These strategies have revealed a surprising diversity in chickpea’s symbionts around the globe. The nature of sampling allows us to infer factors that pattern the distribution of chickpea’s diverse symbionts. Experiments are currently underway in India and Ethiopia to test whether predictions of symbiotic effectiveness of variable strains based on whole-genome sequences bear out in farmer’s fields.