The study was aimed at investigating variations in agro-morphological traits of two selected wheat varieties after chemical mutagenesis using ethylmethanesulphonate (EMS). Two varieties (SST 56 and SST 875) were subjected to EMS mutagenesis using 0.5% v/v EMS at 32.5°C for 1 h. Field trials were carried out at Ukulinga Research Farm of the University of KwaZulu-Natal using a randomized complete block design with two replications. Data on nine important agro-morphological traits were collected and analyzed using the analysis of variance (ANOVA), correlation and principal component analysis (PCA) procedures. Significant variations were found among the agro-morphological traits between M1 individuals of the varieties after the mutagenesis compared to untreated checks. EMS significantly reduced seed germination in the field at 40% in both the varieties and significantly delayed days to heading by eight days. The mutagen caused a shortening of the days to maturity by 13 days in both the varieties. EMS treatment also significantly reduced plant height to 18 and 21cm in SST 56 and SST 875, respectively. The spike length was also reduced by ∼2.5 cm in both the varieties compared to control. 100-seed weight, flag leaf length and seeds per spike significantly increased in the treated seeds of both the varieties. Plant height had positive and significant correlation with number of tillers, number of seeds per spike, flag leaf length and 100-seed weight. However, it had negative correlation with the number of days to maturity. PCA revealed that three principal components (PC 1, PC 2 and PC 3) accounted to 57% of the total variations among the agro-morphological traits in both the varieties. PC 1 alone contributed to 27.7% of the variation which was correlated well with plant height (0.767), tiller number (0.812), number of seeds per spike (0.599) and seed yield (0.720). PC 2 explained 15.6% of the variation and well-correlated with germination percentage (0.784), spike length (0.554) and flag leaf length (0.772). PC 3 accounted to 12.4% of the variation and had negative correlation with days to maturity (−0.730). The study found that EMS had the potential to increase agro-morphological variations in wheat. This could be useful in selecting novel mutants with desired phenotypic traits.