A library of seven novel 1,3-benzothiazole-substituted BODIPY derivatives with tunable optical properties was synthesized. The new fluorescent dyes exhibited bathochromically shifted absorptions (up to 670 nm) and emissions centered in the red and near-infrared spectral region (up to 677 nm) in comparison to the parent compound 8-phenyl BODIPY (λabs: 499 nm, λemi: 508 nm). (TD)DFT calculations were performed to rationalize the spectroscopic properties of the new dyes. The cellular biodistribution of the new BODIPY dyes, their fluorescence stability and toxicity were investigated in both living and fixed fibroblasts using time-lapse fluorescent imaging and confocal microscopy. Six of the seven new dyes were photostable and non-toxic in vitro at 10 μM concentration. In addition, they efficiently stained the cell membrane, showing diffuse and dotty localization within the cell at low concentrations (1.0 and 0.1 μM). Specifically, dye TC498 was localized in vesicular structures in both live and fixed cells and could be used as a suitable marker in co-staining studies with other commonly used fluorescent probes.