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Pearl millet [Pennisetum glaucum (L.) R. Br.] is a staple food crop of arid and semi‐arid regions of Asia and Africa. Forty‐five pearl millet populations of Asian and African origin were assessed for genetic diversity using 29 simple sequence repeat (SSR) markers. The SSR‐based clustering and structure analyses showed that Asian origin–Asian bred (As‐As) and African origin–African bred (Af‐Af) populations were distributed across seven clusters, indicating no strong relationship among populations with their geographical origin. Most of the African origin–Asian bred (Af‐As) populations had a higher average number of alleles per locus than As‐As or Af‐Af populations, and the majority of them clustered separately from As‐As or Af‐Af populations, indicating that introgression of African origin breeding materials led to the development of new gene pools adapted to the Asian region. Fourteen populations representing seven clusters were crossed according to a diallel mating design to generate 91 population hybrids (seeds of direct and reciprocal crosses were mixed) and evaluated at three locations in 2016. All the 91 hybrids when partitioned into three groups based on genetic distance (GD) between parental combinations (low, moderate, and high), revealed no correlation between GD and panmictic midparent heterosis in any of the groups, indicating that grain yield heterosis cannot be predicted based on GD. Two population hybrids (GB 8735 × ICMP 87307 and Sudan I × Ugandi) exhibited high levels of yield heterosis over standard checks and can be further utilized using different breeding schemes to develop high‐yielding pearl millet cultivars. [ABSTRACT FROM AUTHOR]