The nature and magnitude of genetic diversity was assessed using Mahalanobis's D2 statistics and canonical analysis of 10 physiological traits in 50 cultivars of soybean (Glycine max (L.) Merr.) grown in monoculture and intercropping with maize (Zea mays L.). All cultivars were grouped in 10 clusters in monoculture; eight clusters were observed under intercropping. The expression of genetic diversity for physiological traits was greater in monoculture than in intercropping. Some cultivars had similar clustering patterns in both cropping systems, while others were affected by the cropping system in expressing the genetic diversity, confirmed by canonical analysis. Geographical distribution of cultivars was not necessarily reflected by the genetic divergence. The relationship between geographic and genetic diversity was evident under both cropping systems, while other cultivars were similar. Selection on the basis of complementarity of physiological traits to develop varieties suitable for monoculture, intercropping and both cropping systems is suggested.