An interesting group called excavates is considered as one of the keys to understand early eukaryotic evolution. Excavates include jakobids, malawimonas, trimastix, carpediemonas, diplomonads, retortamonas, and heterolobosea. Other relatives have been associated because of their relationship to one or more core-excavate taxa. These relatives include Oxymonads, Parabasalids, and Euglenozoa. Many relationships among excavate taxa and their relatives are uncertain. We present a phylogenetic analysis of the excavate taxa and their relatives using our newly developed quartet-based method (QBNJ). We also demonstrate how molecular phylogenetic methods and morphological evidences can be effectively incorporated into the tree reconstruction. We found that some clusters are robust and independent of the methods used. However, at some point during the merge process there are critical points where more than one possible merge could be possible for the same species/subtree. More reliable results could be obtained by combining morphological and molecular phylogenetic analyses.