Toxoplasma gondii is a protozoan parasite that causes infection in birds and mammals (terrestrial and marine), both domestic and wild. The state of Tabasco has favourable climatic and ecological conditions for the replication and dissemination of this parasite. Therefore, the aim of this study was to isolate and genotype T. gondii from free-range chickens in this region of México by PCR-RFLP of 15 genetic markers. A total of 12 chickens were obtained from 7 municipalities. Serological survey by the modified agglutination test (MAT) of chicken serum samples revealed that 9 out of the 12 chickens (75%) tested had antibodies against T. gondii (titres ≥ 1:10). Toxoplasma gondii DNA was detected by PCR in tissues from 8 out of the 12 chickens. Twelve viable strains of T. gondii were isolated from the heart and brain samples of eight chickens by bioassay in mice. Genetic characterization of tachyzoite-derived DNA was performed using 10 multilocus RFLP-PCR genotyping markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) and five virulence-related markers (CS3, ROP5, ROP16, ROP17 and ROP18). A total of 6 ToxoDB PCR-RFLP genotypes were identified, including #8 (also known as Type BrIII), #28, #38, and 3 new genotypes designated as #344, #345 and #346. Combination of ROP18/ROP5 alleles were 1/3, 3/3 and 4/3. ToxoDB #344 and #345 genotypes also had a new allele at the ROP5 locus. These results suggest high genetic diversity of T. gondii in southeastern México.