This article presents a newly developed capillary gel electrophoresis (CGE) using dynamic coating with hydroxyethylcellulose methodology for the separation of fourteen standard DNA fragments and determination of RAPD-PCR products after a PCR purification clean-up procedure for certain Salvia (sage) species. The developed CGE was successfully applied to the RAPD products of ten different Turkish Salvia (sage) species (Salvia bracteata, S. candidissima, S. ceratophylla, S. dichroantha (endemic), S. forskahlei, S. fruticosa, S. sclarea, S. tomentosa, S. verticillata, and S. viridis). These medicinal plants exhibit a wide range of Turkish flora. The CGE results were compared with those by the slab gel electrophoresis (SGE). The present study offers an alternative CGE method to SGE for the effective separation and evaluation of RAPD-PCR products. This CGE has certain advantages to SGE on the viewpoint of requiring smaller amount of sample and solvent, higher resolution and speed, easier automation, higher sensitivity, and online detection. DNA analysis in Salvia species can help further understanding of their biological functions. In this study, a phylogenetic relationship was analysed by SGE. S. fruticosa and S. dichroantha are genetically the most distant species, and S. bracteata and S. fruticosa are the the most similar species.