The aim of the present study was to detect and genotype T. gondii in free-range chickens destined to human consumption in Alagoas state, Brazil. Methods Two hundred blood samples were collected from free-range chickens and submitted to indirect immunofluorescence antibody test (IFAT). Brain tissue from 14 animals randomly selected were subjected to mouse bioassay. Positive samples in mouse bioassay were submitted to PCR and genotyped by PCR-RFLP. Results Out of two hundred blood samples from chickens, 72 (36%) samples were considered positive by IFAT. Two T. gondii strains were isolated, both being characterized as atypical and classified as #146 and a new genotype, named #279 in ToxoDB database. Conclusions Our results showed a sero-occurrence of T. gondii in free-range chickens intended for humans, and the genetic diversity of the parasite in Brazil, with a new genotype described.