In this work, we described the synthesis of 10 new fluorescent 2,1,3-benzoselenadiazole small-molecule derivatives and their chemical- and photocharacterizations. The new derivatives could, for the first time, be successfully applied as selective live cell imaging probes (at nanomolar concentrations) and stained lipid-based structures preferentially. Density functional theory (DFT) calculations were used to help in understanding the photophysical data and the intramolecular charge-transfer (ICT) processes of the synthesized dyes. Some derivatives showed impressive cellular responses, allowing them to be tested as probes in a complex multicellular model (i.e., Caenorhabditis elegans). When compared with the commercially available dye, the new fluorescent compounds showed far better results both at the cellular level and inside the live worm. Inside the multicellular complex model, the tested probes also showed selectivity, a feature not observed when the commercial dye was used to carry out the bioimaging experiments.