Neuromodulators such as monoamines assure essential brain functions but relatively little is known about their mechanism of release. While recent work has advanced our knowledge of active zone architecture in dopamine axons, release machinery within the synaptic vesicle (SV) remains poorly understood. Here, we address differences between the release of monoamines and classical synaptic transmitters by comparing the composition of SVs that contain the vesicular monoamine transporter 2 (VMAT2) versus vesicular glutamate transporter 2 (VGLUT2). Previous work revealed that these SV populations differ in frequency dependence, recycling kinetics and biogenesis. We now find differences in the abundance and isoform expression of many SV protein families. These findings provide new insights into the molecular diversity of SVs and mechanisms of dopamine release.