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A phylogenetic analysis on specimen level was made in possible support of a multivariate analysis of the Calamus javensis complex. Nine species, at some time recognized within the complex, and several recognisable forms were included. The phylogenetic markers used were the nuclear 5S spacer (5S nrDNA) and the chloroplast Maturase K (matK). The Bayesian analysis showed that only 5S provided some resolution. The 50 % majority rule consensus showed one major polytomy with a few supported groups, which were mainly morphologically unsupported pairs of specimens. However, one group, the form C. tenompokensis (the only distinct group in a multivariate analysis) is morphologically distinct and phylogenetically monophyletic and can be recognized as a species. Of all other recognizable forms, we only consider C. acuminatus to be regarded as a variety as it was not supported in the morphometric analysis.