Soybean is nutritionally rich source of proteins and fats. It is grown in many countries of world including US, China, Brazil and India. Pakistan grows soybean on a very limited land owing to lack of farmers interest and government attention. Soybean lines; B24G14, B23G5, B20G16, B21G2, B21G9, B6G23, B23G16 and B29G11 were grown for one month and analyzed for morphological and molecular variations. In order to analyze genetic variations, Single sequence repeat (SSR) markers were used. The line B20G16 showed the highest morphological growth parameters of plant height, total number of leaves, leaf width, leaf length and leaf weight, while line B29G11 revealed the lowest. The maximum plant height (128.03 cm) was found for line B20G16. A maximum number of 48 leaves with leaf width of 2.34 cm, leaf length of 3.34 cm leaf and leaf weight of 156.11 mg were recorded in line B20G16. The line B29G11 grew with the least plant height (51.01 cm), number of leaves (24), leaf width (1.13 cm), leaf length (2.14 cm) and leaf weight (136.67 mg). Five SSR primers (Soy satt 001, Soy satt 005, Soy satt148, Soy satt160, Soy satt171) which were previously reported to be highly polymorphic and mapped on different linkage groups, were used for analyzing genetic variations in soybean. All the primers were amplified with two different-sized alleles against each primer. Dendrogram was constructed using software SAS by Neighbor-Joining method which clustered the soybean lines into two groups. Maximum genetic dissimilarity (7) was found between line B24G14 and line B23G16. From the results of the study, it was clear that B20G16 had maximum morphological growth, while B29G11 revealed minimum growth among the tested lines, although these two lines were clustered into the same cluster interestingly. It can be concluded that line B20G16 may be further analyzed and might be useful in breeding programs.