Neospora caninum is a world-wide parasite that causes neuromuscular disorders in dogs and bovine abortion. Biological diversity among isolates has been proved in both in vivo and in vitro studies. In contrast, little is known about the genetic diversity of this parasite. Microsatellite sequence analysis constitutes a suitable tool that has been used for the genetic analysis of other apicomplexan parasites. In this report, we describe the identification and analysis of 13 microsatellite loci from N. caninum DNA sequences deposited in public databases, which were evaluated with the use of 9 isolates grown in vitro. One microsatellite was monomorphic, and the remaining 12 loci exhibited 3 to 9 separate alleles. Multilocus analysis showed that each of the 9 isolates investigated here displayed a unique profile and revealed no association between the genetic similarity and host or geographic origin. The multilocus analysis approach described here might nevertheless provide the powerful tool needed to study the genetic complexity of N. caninum and the molecular epidemiology of neosporosis.