The present study aimed to determine the variation in onion and garlic genetic resources collected from the Kelkit Valley, a unique biodiversity concerved region in Türkiye. For this purpose, 17 onion genotypes and 12 garlic genotypes were collected from local growers. A total of 9 biochemical analyses (total phenolic matter, total soluble protein, total dry matter, total flavonoid matter, ferric reducing antioxidant power, cupric reducing antioxidant capacity, 2,2-diphenyl-1-picrylhydrazylradical scavenging activity, hydrogen peroxide scavenging capacity and ascorbic acid) were performed on bulb and leaf extracts of all genotypes. According to variance analysis of the biochemical results from the samples, the differences between genotypes for all parameters were found to be significant (p < 0.05). A post-hoc test (Tukey) and multiple means comparison were performed to analyze the results between groups in cases of significant differences. The results indicated that there is a large variation between different genotypes of both species and between both species and organs.