Comparison for some quantitatively controlled traits viz. number of tillers per plant, flag leaf area (cm2), plant height (cm), spike length (cm), days taken to ear emergence, days taken to maturity, number of spikelets spike-1, 1000-grain wt (g), number of grains spike-1, grain yield plant-1 (g) and drought tolerance using polyethylene glycol (PEG) method; was accomplished for 65 wheat genotypes using cluster analysis for determining phenotypic differences among the genotypes. Based on euclidian distance as a measure of dissimilarity for contrast in the traits and difference in the genetic back ground, eight genetically different genotypes i.e. May-1942, Pari-73, SVP-74, SVP-83, Dera -98, Zam-04, Gomal -08, and Hashim-08 were selected to attempt four cross combination i.e. May-1942 × Dera-98 (cross-1), SVP-74 × Zam-04 (cross-2), Pari-73 × Hashim-08 (cross-3) and SVP-83 × Gomal-08 (cross-4). After developing six basic populations for Joint segregation analysis SA i.e. P1, F1, P2, BC1, BC2 and F2, on the pattern of joint segregation analysis (JSA) the material was planted in three replications into two separate experimental sets i.e. one for determining gene action on quantitatively controlled traits under normal field conditions and the other under artificially created drought conditions in the field. Under normal conditions, genetic effects for the above mentioned morphological traits were determined using JSA of mixed inheritance model consisting of 24 genetic models as statistical approach. The analysis revealed that genetic model D-2 representing mixed one additive major gene and additive dominance polygene was best fitting for some crosses with respect to plant height, spike length, number of spikelets spike-1, number of grains per spike and 1000-grain wt (g). Model D, representing mixed one major-gene and additive-dominance-epistasis polygene was best fitting for flag leaf area and 1000-grain wt in some crosses. Whereas model D-1, representing mixed one major-gene and additive dominance polygene was the only best fitting for plant height in case of cross –2 (SVP-74 × Zam-04). Similarly, model D-4 representing mixed one negative dominance major gene and additive-dominant polygene was the only best fitting model for spike length (cm) in case of cross 2 (SVP-74 × Zam-04. Model E-1 representing mixed two major additive dominance epistatic genes plus additive dominant polygene was best fitting for plant height (cm), number of grains spike-1, days taken to maturity, flag leaf area (cm2), number of tillers per plant, days taken to flowering, grain yield (g) per plant and 1000-grain wt (g) in most of the crosses. Genetic model E, representing mixed two major additive dominance epistatic genes plus additive dominant epistasis of polygene was best fit for days taken to flowering, number of tillers per plant and number of grains spike-1 in few crosses. Whereas, genetic models E-3 representing mixed two major additive genes plus additive-dominant polygene was fitting for number of spikelets spike-1 and number of tillers per plant only in case of cross-2 (SVP-74 x Zam-04).