Modern fluorescence imaging techniques have become essential tools to provide crucial insights in understanding complicated biological processes. Because of their unique optical properties (e.g., excellent photostability, high brightness, broad absorption, and narrow emission), inorganic quantum dots (QDs) have attracted great interest in fluorescence bioimaging. However, the intrinsic toxicity resulting from their heavy-metal components as well as the low-pH-induced fluorescence-quenching phenomenon has motivated researchers to explore novel fluorescent probes with the goal of overcoming these obstacles. In this work, we report the synthesis of two groups of organic fluorescent dots with aggregation-induced emission (AIE) characteristics that have a large Stokes shift, ensuring distinct emission spectra (green and red fluorescence) under singlewavelength excitation. Single-particle imaging experiments revealed the unique optical properties of such AIE dots, which outperform their commercially available inorganic QD counterpart in physical stability and brightness. Upon functionalization with a cell-penetrating peptide, the strong absorptivity, high brightness, good cellular-internalization efficiency, and low cytotoxicity of both the green and red AIE dots allow for the simultaneous discrimination of different populations of cancer cells both in culture medium and animal organs, which is of high importance for understanding cellular interactions during cancer metastasis. Considering the versatile surface functionalities endowed by the encapsulation matrix, a series of organic AIE dots with customized properties will provide prospective platforms to satisfy multifarious bioimaging tasks in the near future.