The Atlantic Forest is among the 35 hotspots on the planet, and yet few floristic or structural studies have been conducted on mature forest fragments of that biome in Brazil. In view of this knowledge gap and of the need to further comprehend the importance of conserving mature forests, we surveyed the arboreal component of three little-altered forest remnants from the S?o Paulo metropolitan region (SPMR), southeastern Brazil, and compared our data with the one from other phytosociological studies performed in the region. Mature forests showed a different floristic composition from one of young forests. Overall, the former has a higher number and percentage of threatened and endemic species than the latter, and also a higher exclusivity of occurrence of threatened species. In areas up to twice as smaller, mature forests have 1.5 to 4.3 times more endemic species to the Atlantic Forest and up to 9 times more species threatened with extinction than young forests. These facts, along with the scarcity of remnants of mature forests, led us to consider such forests as hotspots within the Atlantic Forest hotspot in the SPMR, as well as to categorize them as of high relevance for conservation.