Tree squirrels play an important role in the maintenance of forest ecosystems by functioning as seed and fungal spore dispersers, forest regenerators, and prey for forest predators. The highest species richness for tree squirrels occurs in tropical forests and these species are also the least studied. We conducted distance sampling to estimate population density, measured habitat variables to investigate forest characteristics that influence habitat selection and feeding site selection at three different scales, and conducted observations to obtain knowledge about activity pattern and behavior of Neotropical pygmy squirrels and Amazon red squirrels in the Peruvian Amazon. Density of Neotropical pygmy squirrels was 0.10 and 0.14 individuals/ha for 2009 and 2010. Activity peaked in early morning, squirrels were found mainly in the canopy but never on the ground, and frequency of behaviors differed by time and story level. Neotropical pygmy squirrels used mainly high and low restinga and areas that had more large trees. Squirrels also used species of trees disproportionately to availability. Neotropical pygmy squirrels seem to be associated with features related to mature forests. Amazon red squirrels use mainly high and low restinga and selected Astrocaryum and Attalea palm trees that were taller and larger as foraging sites compared to random locations. Amazon red squirrels used all vertical strata of the forest and the main behaviors observed were travel and forage. Behaviors were similar among time periods but differed in frequency by vertical strata. Although Amazon red squirrels used vegetation communities differently than their availability and selected for tree characteristics, they did not select for site characteristics and this is different from other tree squirrel species. We also conducted surveys during a wet and a dry year to investigate and estimate diversity of diurnal mammals. We assessed the vertical strata of the forest to determine if diversity index varied by story level, and estimated alpha, beta, and gamma diversity. Overall mammal diversity did not differ between wet and dry years. Diversity index differed by story level between years, but was the highest in the canopy for both years. Alpha diversity was higher in the dry year, and gamma and beta diversity were higher in the wet year. Frequency of sightings of species was influenced by time of day and varied by story level. Protection of continuous, mature forests with large canopies has important conservation implications as these areas most likely protect the greatest diversity of mammals while also providing shelter and food for other taxa.