The increase of size and connectivity of forest fragments positively affect bird species number. Here we investigated if variations in the topography, which create valley bottoms and upland areas within the forest fragment, could be also a driving factor. We argue that topography has implications for conservation because forest fragments with higher proportion of valley bottoms could harbor higher bird species number, independently of fragment size. We estimated the number of bird species in 25 forest fragments of Atlantic Forest in southern Brazil. We also mapped the area of valley bottoms in each forest fragment to calculate the percentage of the valley bottom area in relation to the total area of each forest fragment. The results indicate: (1) the percentage of valley bottom area is not correlated with the total area of the forest fragments; and (2) the number of bird species increase with increasing the proportion of bottom valley area and did not respond to total area. These findings suggest the proportion of valley bottoms in a forest fragment is relevant and important for higher species number. Also, high humidity levels in valley bottoms may contribute to enhancing the resilience of forest fragments against the mounting challenges posed by the increasing incidence of forest fires and prolonged dry seasons, a trend intensified by the ongoing effects of climate change. Conservation actions in the studied region should focus on the expansion of the current network of protected areas by combining the inclusion of forest remnants with high proportion of valley bottoms and the restoration of valley bottoms in existing protected areas. Indeed, creating of corridors to connect valley bottoms of forest fragments via riparian forest can improve overall habitat quality.