Members of the family Strongylinae are among the most pathogenic gastrointestinal nematodes infecting equids, causing severe complications such as aneurysm formation and thrombosis within the circulatory system, particularly in the cranial mesenteric artery, which may result in fatal outcomes. Due to the limited number of post-mortem investigations, this study aimed to detect natural infection and identify Strongylinae species infecting local donkeys and horses in Baghdad, Iraq. Adult worms recovered from infected animals were examined using morphological characterization and scanning electron microscopy (SEM). Molecular identification was performed through amplification and sequencing of the internal transcribed spacer 2 (ITS-2) region of rDNA, followed by phylogenetic analysis. The overall prevalence rate of infection was 32.3%. Morphological examination identified three species: Strongylus vulgaris, Strongylus equinus, and Triodontophorus serratus, with S. vulgaris being the predominant species. Phylogenetic analysis of ITS-2 sequences revealed that S. vulgaris isolates from the present study clustered within the same genetic lineage as isolates previously reported from Egypt and Germany, while sequence comparison demonstrated a high degree of similarity with isolates from Iran and Turkey. Partial sequences of S. vulgaris generated in this study were submitted to GenBank under accession numbers PX442251–PX442254. This study represents the first report from Baghdad, Iraq, describing the diagnosis, morphological characterization, SEM-based identification of adult worms, and genetic characterization of S. vulgaris recovered from naturally infected equids.