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The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N. caninum isolates based on multilocus microsatellite genotyping. Currently, the most extensive study reported is based on the N. caninum genotyping of 96 samples from four countries on two continents (Spain, Argentina, Germany and Scotland) that demonstrate different clusters of multilocus genotypes (MLGs) implicated in cattle abortions as well as the population sub-structuring of N. caninum, which is partially associated with the geographical origin. The aim of this study was to genotype N. caninum from aborted bovine foetuses that originated from Mexico within the region of Aguascalientes and to investigate their genetic diversity. Parasite DNA was detected in 27 out of the 63 analysed foetuses recovered from 10 different herds. Complete or nearly complete profiles based on 9 microsatellite markers were obtained from 11 samples. Diverse N. caninum MLGs were implicated in the occurrence of abortion in each herd. All of the Mexican MLGs differed from the MLGs previously determined for the Argentinean, Spanish, German and Scottish N. caninum populations. The Mexican MLGs failed to cluster by eBURST analyses. The MLG relationships using PCoA showed a close genetic relationship between the Spanish population and a portion of the Mexican population, but a more distant genetic relationship with the Argentinean genotypes. These results demonstrate the genetic diversity of N. caninum in the studied areas that differed from other populations of N. caninum around the world. [ABSTRACT FROM AUTHOR]