Maize production and productivity in sub-Saharan Africa are constrained by various factors. Assessing the genetic diversity of newly developed elite inbred lines can help identify lines with desirable genes and explore genetic relatedness for heterotic breeding. The objectives of this study were to assess the level of genetic diversity, and population structure, and identify appropriate clustering methods for assigning maize inbreds into heterotic groups. Three hundred and seventy-six elite inbreds extracted from three source populations were genotyped using Diversity Array Technology (DArTtag) mid-density platform. Results from 1904 of 3,305 SNP marker obtained revealed average marker polymorphism information content (PIC) of 0.39, observed heterozygosity of 0.02, gene diversity of 0.37, minor allele frequency of 0.29, Shannon and Simpson indices of 6.86 and 949.09, respectively, and allele richness of 787.70. The optimum sub-population was three defined by an admixture-based model and principal component analysis. The average genetic distance was 0.303 varying from 0.03 (TZEI 2772 × TZEI 2761) to 0.372 (TZEI 2273 × TZEI 2832). For appropriate heterotic classification of the 376 elite inbreds, the use of IBS distance matrix and average linkage clustering method provided the highest cophenetic correlation coefficient (0.97). Three heterotic group (HG) were identified using IBS distance and average linkage clustering method with HG 1 have 188 inbreds, HG 2 having 137, and HG 3 having 59 inbreds. The pedigree-based phylogenetic tree showed substantial consistency with the heterotic groups identified. The F-statistics based on the underlying population structure revealed 10% variation among sub-populations and 90% variation within sub-populations with a moderate level of genetic differentiation (0.10). The elite inbred lines showed a high degree of genetic diversity, which could be beneficial for developing new, early-maturing white hybrids to mitigate production constraints in sub-Saharan Africa.