This study analyzes intra‐ and interspecific variation in chloroplast DNA (cpDNA) in diploid Triticum‐Aegilops species. This analysis focused on DNA sequence variation in noncoding regions of cpDNA, which included base‐pair substitutions, insertion/deletions (indels, 50 loci pooled), microsatellites (7 loci pooled), and inversions. Nine of 13 Triticum‐Aegilops species were successfully identified and genotyped using these data. Sixty‐two haplotypes were detected in 115 accessions of 13 diploid species. Because of the large number of characters examined, novel deep relationships within and among Triticum‐Aegilops species could be identified and evaluated. Phylogenetic trees for the genus Triticum‐Aegilops were constructed with Hordeum vulgare and Dasypyrum villosum as outgroups, and the results were compared to previous studies. These data support the following inferences: (1) Aegilops species should be included in Triticum; (2) groups D, T, M, N, U, and section Sitopsis (except Ae. speltoides) underwent speciation concurrently, but most diploid species evolved independently; (3) Ae. mutica does not occupy a basal position in Triticum‐Aegilops; (4) Ae. speltoides is in a basal position and differs significantly from other Sitopsis species; (5) Ae. caudata is polyphyletic in all trees; (6) the genus Aegilops is paraphyletic with Secale.