The purpose of the study was to evaluate the possible genetic variation occurred due to the action of transposons. Hibiscus rosasinensis was selected for the study as it had the transposable elements similar to the one found in maize, which can be useful for the differentiation of colors in this plant. In this study an attempt was made to identify the transposable elements and to study the dynamics of the cryptic plant species. The plant DNA was successfully extracted and run with 0.8% Agarose gel electrophoresis. After isolation of DNA specific transposable element primers were used to amplify the 300bp of fragment. These fragments were subjected to RAPD which identified the transposon sequence (106bp) named as En/Spm. These fragments represent ribulose 1, 5-bisphosphate carboxylase large subunit (rbcL) gene which were confirmed with NCBI-BLAST. The sequences were initially aligned with Clustal-X software. Based on this alignment, 224bp of sequence were used to construct phylogenetic tree. Hence, the relationship shows that Hibiscus rosasinasesis (Brown) and Hibiscus rosasinensis (Pink) are closely related, but the Hibiscus rosasinasesis (Red) is distantly related. The same results were shown in RAPD technique when the transposable element sequence was compared with RAPD marker. It can be concluded that the Hibiscus rosasinensis plant has more than 80% of transposons which was responsible for the color changes.