| Summary: | <p>There are eight <em>Exacum</em> spp. (Family Gentianaceae) found in the wild in Sri Lanka namely, <em>Exacum axillare</em>, <em>E. macranthum</em>, <em>E. pallidum</em>,<em> E. trinervium, E. walkerii, E. pedunculatum, E. petiolare</em> and<em> E. sessile</em>, of which four are designated as threatened species. This study was conducted to determine the phylogenetic relationships of four of the endemic Sri Lankan<em> Exacum</em> spp which have shown a potential in the floriculture industry, namely <em>E. trinervium, E. macranthum, E. walkerii</em> and <em>E. pedunculatum</em>. with <em>E. affine</em> (a non-endemic, commercial species) and to compare their sequences of the Internal Transcribed Spacer (ITS) region of 18S-26S rDNA for use as a possible DNA typing target. The study also compared the <em>Exacum</em> spp. of Sri Lanka with the morphologically similar species <em>Osbeckia octandra</em>. The DNA was isolated from tender leaves, the ITS region was amplified by Polymerase Chain Reaction (PCR) and the nucleotide sequences of the PCR products were determined. The amplified products of the ITS region of different species were estimated to be 554-720 bp. Multiple sequence alignment of the ITS sequences were carried out using ClustalW program and phylogenetic relationship of the species was determined by using Mega 4.0.2 package. The two endemic species <em>E. macranthum</em> and<em> E. trinervium</em>, were the closest relatives and clustered together in the phylogenetic tree with <em>E. walkerii. Exacum pedunculatum</em> formed a separate cluster with the exotic species E. affine, diverging from the cluster and branching separately. <em>Osbeckia octandra</em> diverged from all <em>Exacum</em> spp.</p><p>Tropical Agricultural Research Vol. 25 (4): 502 – 511 (2014)</p>
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