Forest flora of Cambodia remained poorly documented, making it difficult to carry out studies on forest composition based on species identification. For example, Kao and Iida (2006) listed 80 species for which scientific names remained undetermined, and Top et al. (2009) listed 88 unidentified species that amounted to 36% of the total 243. Even for identified species, identification often differed among literature. To overcome this difficulty, we applied DNA barcoding to identify species. We collected 603 samples and sequenced rbcL and matK regions. Based on the identification of families and genera of BLAST searched sequences, we further checked taxonomic literature and specimens of major herbaria (Kew and Leiden) to identify species. We identified 349 species including 80 families and 224 genera. Based on this species identification, we performed analysis of phylogenetic community structure using the data of permanent plots. We used 32 plots where 4 times measurements had been finished during 12 years. To reveal the effect of illegal loggings on the phylogenetic community structure, we analyzed rank abundance curve, changes of phylogenetic diversity and species richness during 12 years, factors of illegal logging, phylogenetic relatedness within plots and phylogenetic relatedness among plots. We would like to show the preliminary results of it.