Few studies have examined the relative importance of habitat loss and fragmentation caused by structurally complex matrices such as plantations. We examined the effects of the loss and fragmentation of the original deciduous habitat (secondary deciduous broadleaf forest) caused by a larch plantation matrix on bird occurrences in deciduous habitats in both the winter and breeding seasons in Chikuma Highland, Nagano prefecture, central Japan. Birds were counted using the plot-count method in 33 (winter) and 51 (breeding) deciduous habitats with a range of surrounding habitat loss and fragmentation at a 1600-m scale. Three species groups, for which larch plantations are likely to function as low-quality matrices, were analyzed. Effects of landscape structure were found only for flycatchers, which were negatively affected by habitat fragmentation. Flycatchers frequently occurred in habitats surrounded by elongated habitat patches in which between-patch distances were short. This effect was significant after the confounding effects of habitat structure were removed. Because habitat fragmentation was more important than habitat loss, the destruction of habitat connectivity, i.e., isolation and contraction of habitat patches, may not be compensated by the amount of habitat and may primarily be considered in low-contrast landscapes.