There are few reports about characterization strains of Toxoplasma gondii that analyze the differences between isolates from Europe or United States with those obtained in South America. The current study analyzes virulence data from the mouse model, the gene SAG2 polymorphism by PCR-RFLP and microsatellite analysis in a single Colombian isolate. The strain was isolated from blood of a child with congenital toxoplasmosis, living in Armenia, Colombia. Analysis of virulence in the mouse showed that this strain has an LD100 of 10 tachyzoites. Both methods of genetic characterization demonstrated that this strain belonged to the clonal type 1 and was called HOM/CTCO/2002/CIBMUQ/BL/HDC (brief name: CIBMUQ/HDC). The CIBMUQ/HDC strain is the first Colombian strain available as a reference strain for national and international researchers.