Oral mucosa under physiological condition contains a certain degree of chromic variation. Differentiating such physiological variations from pigmented lesions appears challenging without a histopathological confirmation. In several oral lesions, pigmentation is a part of the primary pathology or a secondary change to an existing entity. The pigments involved in both physiological and pathological conditions can be broadly categorised as exogenous or endogenous. Among these, melanin accounts for the majority of black to brown pigmentation including malignant melanoma. Clinically, their biological behaviour shows an ambiguity which makes it challenging to arrive at diagnosis for even the experienced practitioner. Although biopsy confirms and reassures the patient, it is impractical to biopsy all pigmented lesions. The standard diagnostic algorithm given below is to aid the clinician to diagnose and treat this diverse group of lesions.