Two indigenous Maltese grape vine varieties (cv. Gellewza and Girgentina) juice extracts were studied for their physicochemical properties at three different locations on the Island of Malta. The mean acidity for Gellewza and Girgentina was 2.729±0.088 and 3.971±0.179 g/L, pH was 4.026±0.039 and 3.704±0.042 and a %Brix was 17.913±0.364 and 17.531±0.189, indicating similarities between the variety-location combinations. Spectroscopic analysis revealed significant difference between the two varieties. The Gellewza variety exhibited a high colour index (3.055-10.774) while the Girgentina variety showed a high tonality ratio (2.656-3.111). Although, the total polyphenolic content of the two varieties was not significant differently in most cases (754.771-2643.552 mg/kg), the red grape Gellewza had significantly higher anthocyanin content (708.236±68.451 mg/kg) compared to the white grape Girgentina (14.412±1.119 mg/kg). Principal component analysis confirmed the differences between the varieties and also exhibited distinctive location differences, based on their physicochemical characteristics.