In order to explore and reconstruct the phylogenetic relationships between Hydrangea and its related genera, we selected a total of 61 species from them on a global scale for the phylogenetic analysis based on the nuclear ribosomal internal transcribed spacer (ITS) and three chloroplast DNA fragments (rbcL, trnLF, atpB). Our results suggest that there is little difference between the phylogenetic trees based on the nuclear gene fragment and the chloroplast DNA fragments, respectively. As a result, by further analyzing the phylogenetic tree based on the combined dataset from both of them, two major clades in Hydrangea. We were identified, which were strongly supported by the morphological evidence that is whether the end of the fruit is truncated or not. Moreover, our results suggest that four groups were supported in each major clade and a total of eight groups were identified in Hydrangea. Some groups received strong support from generalized morphological characters. For instance, the first group was supported by morphological characters of leaf shapes, pollen grains and seed coats. Phylogenetic analyses conducted by this study shed new lights on the understanding of relationships among Hydrangea and its related genera.