Significance To circumvent our dependence on photoactivation in single-molecule microscopy, we devise a universal genetic system to precisely control copy number of fluorescently labeled molecules in a cell. Combined with photostable labels, this system enables long-term single-particle tracking of densely packed cellular organelles and proteins. This strategy expands spatiotemporal length scales of live-cell single-molecule measurements to quantitatively understand complex control of molecular dynamics in vivo.