Rice is a modern short-day plant but equally flower during non-inductive long-day condition due to the possession of second florigen, Rice Flowering Locus T1 (RFT1). RFT1 is an ortholog of Arabidopsis FT gene which triggers flowering induction under long-day (LD) condition. The gene isolation from Malaysian upland rice cv. Wai that induces flowering were reported. Nucleic acids isolation and amplification of the RFT1 were observed, then phylogenetic relationship among other 5 indica and 1 japonica rice were inferred by comparing the gene amino acids sequence data sets using multiple sequence alignment databases. The amplicon quality result indicated that the gene was fully amplified at above 0.5kb, whereas the sequence alignment revealed that the RFT1 gene was partially amplified based on the gaps identified. Among the 6 indica cultivars sequence aligned, they were almost all conserved except on only 12 amino acids. While the cladogram tree result classified the cultivars into three major groups and include Wai under clade that contains both indica and japonica cultivars. This finding concluded that the cultivars are of high evolutionary relationship and well established their molecular relationship. The cultivars relationship provides necessary information for better understanding of molecular evolution and designing scientific breeding system for generation of new rice cultivar.