This study was conducted to investigate the genetic diversity of bread wheat, durum wheat and triticale using agronomic and physiological traits. Morphological and physiological diversity of 23 parents and 53 hybrid were evaluated using a randomized complete block design replicated two times at Research Farm of College of Agriculture, Isfahan University of Technology, located at Lavers, Najaf-Abad in 2016-2017. Also, genetic diversity of 24 genotypes was evaluated in two Lavarak and Asheghabad locations using analysis of variance with a randomized complete block design layout in place. In the first experiment, agronomic traits including days to flowering, days to pollination, days to maturity, plant height, spike length, number of spike per plant, number of grain per spike, grain weight per spike, 1000 grain weight, grain yield per plant, and physiological traitss contain minimum fluorescence, maximum fluorescence and quantum efficiency of photosynthesis II, and in the second experiment, in addition to the above mentioned traits, test weight, biological yield and harvest index were measured in all genotypes . In the first experiment, the results of analysis of variance showed significant differences among genotypes for all the traits studied. grain yield per plant, number of spike per plant, plant height and grain weight per spike had the highest phenotypic variation coefficients, respectively. Study of correlation analysis indicated that number of spike per plant, grain weight per spike, 1000 grain weight had a positive and significant correlation with grain yield per plant. Based on linear regression relationships, it was found that two grain weight per spike and number of spike per plant were linearly correlated with grain yield per plant. Based on stepwise regression analysis using grain yield per plant as dependent variable, number of spike per plant and grain weight per spike were justified 56 and 40 percent of yield variation, respectively. In the factor analysis, four hidden factors were identified which named the maturity period, photosynthetic, economic and spike factors, respectively. Cluster analysis of genotypes based on agronomic and physiological traits divided the genotypes into 6 groups. Estimation of heterosis value based on superior parent and mid- parent for grain yield per plan indicated that hybrid 58 resulting from cross 58 (Long Spike 5 × Roshan) had the highest positive heterosis. In the second experiment, the combined analysis results showed that the effect of genotype for all traits was significant, except for maximum fluorescence. In all studied traits, phenotypic and genetic variation coefficients did not considerably differ for most of the traits, indicating the prominent genetic effects on these traits. The results of correlation coefficients showed that there is a positive and significant correlation between grain yield with number of spike per plant, biological yield and harvest index. There was a linear relationship between grain yield with harvest index and biological yield. Factor analysis revealed four hidden factors that justified a total of 66.47 percent of the variation in the experiment. These factors were introduced as maturity period, spike characteristics, yield and photosynthesis, respectively. The cluster analysis of genotypes based on the studied traits divided the genotypes into four groups, some of which have desirable traits and are desirable for the breeding goals. Keywords: diversity, morphological traits, yield, wheat, environment, heterosis