Whereas matrix management has recently been suggested as a useful tool in biodiversity conservation, patterns and processes within matrices remain unknown. We examined the effects of the loss and fragmentation (configuration) of original deciduous habitats on birds in larch plantation matrix in the winter and during the breeding season in a montane region in Nagano Prefecture, central Japan. Birds were counted using a plot-count method from 32 (winter) and 46 (breeding) matrix (plantation) sites with a range of surrounding habitat loss and fragmentation at a 1600-m scale. Birds were assigned to species groups based on ecological traits, and three groups for which larch plantation would function as low-quality matrix were analyzed. Bird occurrences were explained primarily by habitat structure. Although the effects of landscape structure were less than those of habitat structure, three of five groups across the two seasons experienced significant landscape effects. All effects were of habitat fragmentation (scatteredness of deciduous habitats), i.e. two groups (flycatchers in the breeding season and tree nesters in both seasons) frequently occurred in matrix surrounded by highly scattered deciduous habitats. However, most of these effects were confounded by local habitat structure. That is, the variation in bird occurrences explained purely by fragmentation variables was <6%. Nonetheless, because these effects were marginally significant at p<0.10, there was some support for fragmentation effects after covariation with habitat structure was considered. Based on these results and associated theoretical studies, we hypothesized that habitat fragmentation leads to loss of individuals and is more important than habitat loss in landscapes with a structurally similar matrix. We also hypothesized that matrix within landscapes with highly scattered habitats should be managed with high priority.