Understanding the detailed feeding ecology of endangered animal species is essential for their conservation. However, characterizing their diets is difficult task in wild condition. DNA barcoding technique makes it possible to establish the diet of an individual from its feces and may provide more detailed information than other traditional methods for diet analysis. Using DNA barcoding technique, we tried to detect food plants of the red-headed wood pigeon Columba janthina nitens, which is an endemic subspecies of the Ogasawara Islands and listed as “Critically Endangered”. First, we made a DNA barcoding database of chloroplast trnL (UAA) intron P6 loop sequences from 230 seed plant species grown in the Ogasawara Islands. Second, we performed high-throughput pyrosequencing for 52 fecal samples and identified plant species based on DNA sequences found in the faces. In the P6 loop database, about 70 % of plant taxa could be identified at species level. However, species belonging to some families such as Lauraceae exhibited low variation in P6 loop. Additional barcode markers targeting specific family may complement the approach using trnL. We will also discuss the results of fecal analysis and availability of DNA barcoding technique for diet analysis of the red-headed wood pigeon.