A phylogenetic analysis of Euphorbia is presented using sequences from nine species of nuclear ribosomal DNA ITS and 28S rRNA. Euphorbia is among the largest genera and most diverse of four recently recognized subgenera within Euphorbia, with about 2000 species that are renowned for their remarkably diverse growth forms. Relationships within this group have been difficult to discern due mainly to homoplasious morphological characters and inadequate taxon sampling in previous phylogenetic studies. To clarify phylogenetic relationships in the genus, we used Maximum Parsimony (MP) and Bayesian Inference (BI) analyses. The combined analysis of two molecular markers resulted in only one most parsimonious tree and also generated new supported clades, in general, the backbone of the ITS tree from the concatenated matrix is better supported than 28S rRNA tree, although the order of divergence among the constituent clades is different and the topology is better supported and it resolves most of the same subclades that is common between them. It's concluded that the first comprehensive investigation on the genetic variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.