I studied allozymic variation in five species of Amazonian birds at two geographic scales. At a local scale (all sites within 200 km of one another), I included samples from six sites, three within continuous forest and three in natural forest fragments thought to be several thousand years old. I examined both genetic variation and differentiation to determine whether there were genetic effects related to forest fragmentation. At this local scale, I found little evidence in the allozymic data that clearly suggested genetic structure had been affected in any uniform pattern among species. However, there was genetic differentiation at this level and estimated gene flow (Nm_est from private alleles) was low relative to what is reported in other avian studies. At the regional level, I compared samples from sites that were 500–1,500 km from one another from two Amazonian areas of endemism (Inambari and Rondônia). Four of the five species exhibited substantial differentiation between samples from the two areas of endemism, consistent with other studies of genetic differentiation in Neotropical forest understory birds.