Genotyping of Toxoplasma gondii in different regions of Brazil has shown high diversity and high frequency of virulent genotypes among Brazilian animals. The aim of the study was to characterize samples of T. gondii isolates obtained from naturally infected sheep, goats, pigs and free-range chickens slaughtered for human consumption in Rio Grande do Norte, Northeast Brazil. Nineteen T. gondii samples (isolated from 1 goat, 5 pigs and 13 free-range chickens) were genotyped. Six different genotypes were identified, including two novel genotypes. The archetype genotypes, i.e., types I, II and III, were not found. In mice, seventeen isolates (89.5%) were classified as virulent, and only two (10.5%) were classified as avirulent. This study displays the genotypic variability of the parasite in Northeast Brazil.