To understand the polyamine (PA) catabolic pathways in Brachypodium distachyon, we focused on the flavin-containing polyamine oxidase enzymes (PAO), and characterized them at the molecular and biochemical levels. Five PAO isoforms were identified from database searches, and we named them BdPAO1 to BdPAO5. By gene expression analysis using above-ground tissues such as leaf, stem and inflorescence, it was revealed that BdPAO2 is the most abundant PAO gene in normal growth conditions, followed by BdPAO3 and BdPAO4. BdPAO1 and BdPAO5 were expressed at very low levels. All Arabidopsis thaliana and rice orthologs belonging to the same clade as BdPAO2, BdPAO3 and BdPAO4 have conserved peroxisome-targeting signal sequences at their C-termini. Amino acid sequences of BdPAO2 and BdPAO4 also showed such a sequence, but BdPAO3 did not. We selected the gene with the highest expression level (BdPAO2) and the peroxisome-targeting signal lacking PAO (BdPAO3) for biochemical analysis of substrate specificity and catabolic pathways. BdPAO2 catalyzed conversion of spermine (Spm) or thermospermine to spermidine (Spd), and Spd to putrescine, but its most-favored substrate was Spd. In contrast, BdPAO3 favored Spm as substrate and catalyzed conversion of tetraamines to Spd. These results indicated that the major PAOs in B. distachyon have back-conversion activity.