The SSU rRNA gene has been the most sequenced molecule from various eukaryotes and the SSU rRNA phylogeny is still a useful tool for tracing the evolutionary history of eukaryotes and for elucidating phylogenetic positions of newly discovered organisms and environmental sequences. However, SSU rRNA tree with comprehensive taxon-sampling from eukaryotes hasn’t been reported for a decade. Here, an updated comprehensive SSU rRNA phylogeny of Eukaryota was reconstructed using the maximum likelihood method for the first time. The resulted tree roughly agreed with those that have recently been reconstructed with various multigene datasets and recovered many of major eukaryotic groups as monophyletic lineages, though some of those did not gain good support by bootstrap probability value and the relationship among major lineages was not well resolved. The major eukaryotic groups that were not recovered were Excavata, Hacrobia, Amoebozoa, and Archaeplastida. The present updated SSU rRNA tree provides a current version of SSU rRNA phlogeny and can be used as a reference tree for various researches on the phylogeny, evolution and diver-sity of eukaryotes.