Tumour-initiating cells (TICs) have been identified in many solid human tumours, including malignant melanoma. In this study, an enriched TIC population was identified in two canine malignant melanoma cell lines (CML1 and CML6M) using cell surface markers and functional assays, including the sphere forming assay, aldehyde dehydrogenase (ALDH) assay, reverse transcriptase-polymerase chain reaction and γH2AX staining for double-stranded DNA (dsDNA)break identification and repair. The CD34− population of cells in both cell lines expressed stem cell genes, such as Oct4, Nanog and Ptch1, were more efficient at making spheres in adherence-free media conditions and were able to repair dsDNA breaks faster than the CD34+ population. A subpopulation of cells with high expression of ALDH was identified in both cell lines by flow cytometry. The findings indicate the presence of TICs in two canine malignant melanoma cell lines.