Small woodpeckers have weak excavation capabilities presumed to be affected by tree characteristics. To determine the features of trees preferred by the Japanese Pygmy Woodpecker Dendrocopos kizuki, we compared 50 excavated trees (8 for nesting, 10 for roosting, and 32 old cavities) with 280 unused trees in a natural mixed forest in Hokkaido, Japan. The woodpeckers tended to excavate cavities in larger trees, and preferred decaying trees over living trees. Dominant tree species, such as birches Betula platyphylla and oaks Quercus crispula, tended to be avoided in favour of particular trees especially alders Alnus hirsuta. These results suggest that small woodpeckers select particular trees, with softer wood, in which to nest and roost on the basis of their weaker excavation ability.