Neospora caninum (N. caninum) is the etiologic agent of neosporosis, a potential cause of severe reproductive disorders in cattle, small ruminants, equines, wild animals and canids across the world. The current study is performed to estimate molecular prevalence of N. caninum in small ruminants and equines that had abortion in Kurdistan region of Iraq. A total of 64 tissue samples (brain, placenta, heart, lung and liver) were taken from aborted foetuses, with a total of 122 dam blood samples taken from 63 sheep, 39 goats, 12 mares and 8 jennies in local breed fields. Besides, a risk factor analysis for N. caninum positive animals was performed. The observed prevalence of N. caninum DNA in the blood of sheep, goats, horses and donkeys were 20.6%, 17.9%, 21.4% and 25.0%, respectively, and 19.3%, 17.6%, 18.1 and 20.0% in the aborted foetuses of the animals, respectively. Moreover, occurrence of N. caninum was 20.3% in the blood of aborted dams, while it was 18.7% in their aborted foetuses. Confirmatory analysis was also done through constructing a phylogenetic tree to compare the partial sequences of the Nc-5 gene in our isolates (OP771519, OP771520, OP771521 and OP771522) with the GenBank sequences. This showed 98-100% sequence identity with other N. caninum strains in the GenBank database. Older small ruminants and equines had a higher risk of being positive for N. caninum and exposure to dogs were considered as significant risk factors for N. caninum infection in the studied animals (p<0.05). Thus, the results of this study suggest that N. caninum is one of the microbial abortive agents in small ruminants and equines in Kurdistan region of Iraq. It is hoped that the results of this study will help to control animal abortion in livestock and reduce the economic losses.