The properties of non-GM soybeans with lipoxygenase (LOX) free genotypes, such as Gaechuck#1 (black, LOX2,3-free), Gaechuck#2 (yellow, LOX2,3-free) and Jinyangkong (yellow, LOX1,2,3-free), were compared to Taekwangkong (yellow, LOX1,2,3-present) as control. Length and weight of soybeans were significantly longer in Gaechuck#1, but LOX free genotypes of yellow beans was smaller than Taekwangkong, in terms the size and weight. After soaking for 12 hr, increased ratios of soybean weight were 217.07~226.55%, and they were significantly higher in Gaechuck#2. The total color difference (ΔE) to Taekwangkong was the highest in Gaechuck#1, but another yellow soybean were similar. Crude lipids content was significantly higher in Taekwangkong (17.30%), and these LOX free genotypes (13.71~14.66%) did not show significant difference. Crude protein contents were significantly higher in Gaechuck#1 (34.79%) compared to the other soybeans (32.93~33.47%). Contents of glutamic acid among the detected composition amino acid were highest, and its total contents were highest in Gaechuck#1 (32.42 g/100 g), and the total content of Gaechuck#2 was similar to Taekwangkong. Contents of total isoflavone were higher in LOX free genotypes than Taekwangkong, especially significantly higher in Gaechuck#1 (1672.54 μg/g). Contents of total phenol were highest in Gaechuck#1 (276.91 mg/100 g), and flavonoids content of Gaechuck#1 (26.93 mg/100 g) was 2.6~2.8 times higher than the other samples. DPPH, ABTS radical scavenging activities and reducing power were significantly higher in Gaechuck#1. The yield of soybean curd from tested samples was the highest in Gaechuck#2. Gaechuck#2 as LOX free genotypes was similar to Taekwangkong with regard to physicochemical properties and antioxidant activities. Therefore, we propose that Gaechuck#2 is a more suitable genotype for soybean curd products.