Bucephalandra is a genus of endemic plants in Borneo. It is highly valued in the aquascape community because of its significant economic potential. This study aims to identify the species type of six Bucephalandra sp. accessions from Borneo through morphological characterisation, and evaluate their genetic diversity using maturase K (matK), internal transcribed spacer (ITS) and ribulose-biphosphate carboxylase/oxygenase large subunit (rbcL) markers. The observed characters include the morphology of the leaf, stem and root. Phylogenetic trees were constructed using the unweighted pair group method with arithmetic mean based on each matrix of the respective marker and on the concatenated matrix of all markers. The characteristics of the leaves, stems and roots vary among the six accessions. All accessions exhibit similar leaf colours, except for B. diabolica, which has reddish leaves. The accessions are identified as B. goliath, B. forcipula, B. diabolica, B. kishii, B. pubes and B. minotaur. Based on respective ITS and matK sequences, the tree clusters all Bucephalandra species into three groups. The tree, based on concatenated sequences, not only clusters them into three groups but also differentiates B. motleyana (as reference accession) from other Bucephalandra species. The concatenated data set has a haplotype diversity of 1 and a high level of Pi of 0.10917. It indicates that using matK, ITS and rbcL in combination is an optimal and efficient method for differentiating and clustering the Bucephalandra species. © 2025 by Maejo University, San Sai, Chiang Mai, 50290 Thailand.