Background: Strangles is a highly contagious equine respiratory disease caused by Streptococcus equi subsp. equi. It is a globally significant pathogen and one of the most common infectious agents in horses. In Iraq, no sequencing data on this pathogen are available, and only two molecular studies have been published to date. This study provides preliminary insights into strain diversity and provides a foundation for future large-scale investigations. Aim: This study aimed to investigate the molecular characteristics, identify SeM gene alleles, and perform a phylogenetic analysis of S. equi isolates from horses in Baghdad, Iraq. Methods: We analyzed 59 Streptococcus spp. isolates previously obtained from equine clinical samples. Conventional PCR targeting the SeM gene was used to identify S. equi. Additionally, nine PCR-positive SeM gene products were sequenced, followed by phylogenetic analysis and allele identification. Results: We confirmed 49 isolates as S. equi from the 59 isolates according to the molecular assay. Additionally, nine PCR products were used for sequencing and allele typing of the SeM gene which provided the initial report of SeM-97 allele identification in Iraq. Phylogenetic analysis along with SeM gene typing revealed a close relationship between the Iraqi strains and one Iranian strain with 100% sequence identity, revealing important epidemiological relationships that may indicate regional ties to the strain detected in Iran. Conclusion: The present study represents the first investigation of SeM allele typing in Iraq, identifying the SeM-97 allele of S. equi along with its unique amino acid variations. The findings highlight genetic similarities between Iraqi isolates and a strain from Iran, suggesting the potential regional dissemination of S. equi.