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ABSTRACT When assessing fragmentation effects on species, not only habitat preferences on the landscape scale, but also microhabitat selection is an important factor to consider, as microhabitat is also affected by habitat disturbance, but nevertheless essential for species for foraging, nesting and sheltering. In the Atlantic Rainforest of Brazil we examined microhabitat selection of six Pyriglena leucoptera (white‐shouldered fire‐eye), 10 Sclerurus scansor (rufous‐breasted leaftosser), and 30 Chiroxiphia caudata (blue manakin). We radio‐tracked the individuals between May 2004 and February 2005 to gain home ranges based on individual fixed kernels. Vegetation structures in core plots and fringe plots were compared. In C. caudata , we additionally assessed the influence of behavioural traits on microhabitat selection. Further, we compared microhabitat structures in the fragmented forest with those in the contiguous, and contrasted the results with the birds' preferences. Pyriglena leucoptera preferred liana tangles that were more common in the fragmented forest, whereas S. scansor preferred woody debris, open forest floor (up to 0.5 m), and a thin closed leaf litter cover which all occurred significantly more often in the contiguous forest. Significant differences were detected in C. caudata for vegetation densities in the different strata; the distance of core plots to the nearest lek site was significantly influenced by sex and age. However, core sites of C. caudata in fragmented and contiguous forests showed no significant differences in structure. Exploring microhabitat selection and behavior may greatly support the understanding of habitat selection of species and their susceptibility to fragmentation on the landscape scale.