Flowering time is one of the important target traits in a soybean breeding program. Photoperiod and temperature influence the vegetative and reproductive development from emergence to maturity in soybean. The objective of this study was to analyze genetic variation in flowering time based on agronomic performance and SSR marker. One hundred and eight soybean cultivars evaluated in this study were collected from different geographic regions such as China, Japan, Korea, and Vietnam. Days to flowering and maturity were recorded in the two different field in Suwon, Korea (127^o02’ E longitude, 37^o26’ N latitude), and Can Tho, Vietnam (105^O54’E longitude and 10^O9’N latitude). Genotype data were also collected at one-hundred and twenty six SSR loci. Genotypic variation was observed in flowering time. Vietnamese cultivars were more sensitive to daylength. There was a large variation of maturity among cultivars. Chinese cultivar group was more diverse than the other groups. Through 126 observed loci, the number of amplified bands was common from four to six bands. R² value used to estimate linkage disequilibrium (LD), varied according to LGs. It depended on the distance and number of observed loci. 18 loci were associated closely with flowering time as well as maturity at p < 10^-4. Cluster analyis, based on Nei’s distance and Bayesian method, revealed that Vietnamese and Korean cultivar groups were quite different from the other groups; meanwhile Chinese and Japanese cultivar groups were close. These results will be useful for soybean variety improvement program in future.