Bitter melon or bitter gourd (Momordica charantia L.) of the Cucurbitaceae family is valuable plant for their nutritive and medicinal properties. In this study, molecular, morphological and some biochemical properties of 12 bitter gourd genotypes from different parts of Turkey were determined. Considerable morphological variation among the genotypes was observed for fruit properties such as fruit length (9.33 to 14.33 cm) and time for maturity (late June to late September). For molecular caharacterization fifteen ISSR primers were produced, on average, 113 bands in the accessions were examined and 59 (52%) of them were detected as to be polymorphic, which resulted in a Jaccard's similarity range from 0.80 to 0.98. According to biocehmical analyses, palmitic, stearic, oleic, linoleic and eleostearic acids were detected as the major fatty acids in the studied bitter gourd seeds. Eleostearic acid had the highest proportion among the fatty acids (42.66-61.99%). The bitter gourd genotypes showed different fractions of vitamin E. G1 contained alpha, gamma and delta tocopherol, while G2, G18, G19 and G24 contained only gamma and delta tocopherols. Beta carotene was also present in all genotypes and the ratio was between 56.57 and 116.75 mg/kg. In addition, the genotypes were evaluated for their mineral composition and phosphorus was the major mineral for the genotypes and only sodium was not observed in all genotypes among the studied minerals. This study provided useful information for nutritional perspective of bitter melon and also breeding studies.