An intraspecific chromosomic divergence in Batrachyla antartandica from eight localities of southern Chile indicated polymorphic patterns in C-heterochromatin (C-bands), secondary constrictions (SC) and argyrophilic nucleolus organizer region (Ag-NOR). Four cytotypes based in C-bands patterns in all range of B. antartandica were detected. In addition, the eight localities analyzed showed different patterns in SCs and Ag-NORs distribution. With one exception, there was always correspondence between SCs and Ag-NOR locations. Hypotheses explaining these intraspecific variations are proposed. The value of C-heterochromatin and SCs/Ag-NOR in microevolutionary processes at chromosome level as well as specific markers in frogs is discussed. Additionally, the karyotype of this species is re-described.