Amazonian rainforests are among the most species-rich terrestrial habitats on Earth. The aim of this study was to analyze phylogenetic diversity (PD) patterns of orchid bee assemblages along a latitudinal gradient of 15° from northern Peru to central Bolivia and to relate them to climatic factors and geological history. We expanded an existing phylogeny of orchid bees and analyzed the PD of 15 orchid bee assemblages along a latitudinal gradient using mean pair-wise phylogenetic distance. The resulting pattern was correlated to climatic factors and elevation. We found a hump-shaped pattern of PD that peaked in central Peru and decreased towards the equatorial and especially towards the southern, subtropical sites. The decrease in PD towards higher latitudes is a common pattern found in many taxa, which in our case correlates with increasing climatic seasonality. However, the decrease towards the equatorial sites is unusual and may be related to a particular historic event: the northern sites with low PD are situated in the area of the former Lake Pebas, which covered western Amazonia until 3 mya. After the lake disappeared orchid bees mainly belonging to two distantly related species groups apparently colonized the region and diversified, which led to the comparatively low observed PD. In contrast, in central Peru, no in situ radiations were detected, hence the assemblages were composed of species from diverse phylogenetic lineages. Additionally, we identified multiple phylogenetically independent radiations of regionally restricted Euglossa species along the latitudinal gradient that, according to a published, dated phylogeny, diversified roughly 3–1 mya. The hump-shaped latitudinal pattern of PD of the orchid bees of western Amazonia thus appears to have resulted from a preponderance of early divergent lineages in central Peru and of young radiations from distantly related clades colonizing higher latitudes, possibly triggered by historic climate fluctuations and major geological events.