One or more distinct copies of emm genes lie within a gene cluster that is located downstream from a transcriptional regulatory gene (mry). Mry is a positive regulator for the genes in this cluster and for the downstream gene, scpA. The objective of this study is to examine the structure of this cluster and the distribution of specific alleles within the cluster among group A streptococcal isolates of 32 different serotypes. The peptidoglycan (PG)‐spanning domain, which exists in four divergent forms, was used to identify specific alleles of the genes within the emm cluster. Gene content of the cluster was determined by Southern hybridization with allele‐specific oligonucleotides. Five different chromosomal patterns for this cluster were observed. Sequence heterogeneity in the adjacent mry locus was demonstrated by the ability of some of the isolates to hybridize with a whole mry gene probe, but not with mry‐based oligonucleotide probes. A PCR‐based chromosomal mapping technique was used to examine further the gene order within the emm gene clusters. Structural heterogeneity of the emm gene cluster was found within class I isolates in this study, while class II isolates were relatively homogeneous at this chromosomal locus and distinct from class I.