The starch synthase (SS) gene is one of the genes involved in the starch biosynthetic pathway. The expression level of SS regulates the starch quality and quantity in cassava. Therefore, the characteristics of SS in terms of nucleotide variations and its protein structure need to be identified using bioinformatics tools as the initial step to develop a cassava improvement strategy in the future. The nucleotides length and phylogenetic tree were constructed based on SS sequences of Manihot esculenta, Ipomea batatas and Solanum tuberosum showed low SS nucleotide variation. Characteristics of the motif and protein domain of starch synthase are derived from Glycosyltransferase 5 and 1 in Rossmann fold protein motifs. Characteristics of the secondary structure of starch synthase subunits comprised of the alpha helix, extended strand, and random coil structures. The starch synthase subunits of cassava tubers have predicted secondary structures ranging from 173-524 alpha-helix, 83-161 beta-sheet, and 321-574 random coil. The identity of the starch synthase subunit sequences of cassava is considerably high, with a similarity index of 50-82% compared to the homolog structure template. The identified physicochemical characteristics were instability index, aliphatic index, and GRAVY which all indexes showed varying values.