Despite a 79% reduction in deforestation rates since 2004 in the Brazilian Amazon, the current gross forest loss of 6207 km2 year−1 remains significant, promoting continuous habitat fragmentation. This study assessed the status of forest fragmentation in 2014 across the Brazilian Amazon applying a Morphological Spatial Pattern Analysis (MSPA). Our analysis provides the first 60-m-resolution fragmentation map for the entire Brazilian Amazon, including not only the commonly evaluated fragmentation classes such as core, edge and islet, but also four specific metrics measuring the effects of fragmentation on forest patterns (perforation, bridge, loop and forest branches). Areas of intense forest fragmentation were detected not only along the “arc of deforestation” of the eastern and southern Brazilian Amazon but in other regions as well. Considering a 1020-m edge width, we found that 28% (~891,000 km2) of the remnant forest was in non-core classes. Among these classes, bridge (i.e., forest corridors too narrow to contain core area) was the most representative (10.8%). The proportion of core area varied greatly among states, from 82.8% of the remaining forest in Amazonas to 26.1 and 13.5% in Maranhão and Tocantins, respectively. The detailed diagnosis of tropical forest fragmentation is a critical step for proposing solutions to maintain the stability of tropical forest services, including carbon storage, water and nutrient cycling, and biodiversity.