Several inbred strains and a certain percentage of wild mice bear a deletion in the E alpha gene of the mouse major histocompatibility complex (H‐2). This mutation prevents transcription of the E alpha gene and hence functional expression of the E alpha E beta dimer on the cell surface. Two strains were selected for a more precise localization of this deletion. BALB.B is a congenic line carrying the H‐2b haplotype on the BALB/c background. CRO435 is an outbred stock derived from a wild mouse captured near Cairo, Egypt; it carries the H‐2w37 haplotype including a null Ew28 alpha allele, as well as semi‐lethal mutations in the H‐2 linked t complex (tTuw7). From these two strains, we have isolated genomic clones that contain fragments spanning the E alpha deletion, and have sequenced the breakpoint region. The deletions in the two strains are identical, spanning 627 bp which include the promoter region and the signal peptide exon of the E alpha gene. Limited sequence comparison suggests that the Eb alpha allele of BALB.B is more closely related to the Ew28 alpha allele of CRO435 than both of these are to an E alpha‐expressor allele, Ed alpha. It is therefore likely that the Eo deletions in the various inbred strains and wild mice are of the same origin, and we propose that they have been disseminated throughout the mouse population because of linkage to the t complex.