Fluorescent dyes (especially photoconvertible cyanine dyes) are traditionally used as labels to study single-cell or cell-group interactions and migration. Nevertheless, their application has some disadvantages, such as cytotoxicity and dye transfer between cells during co-cultivation. The latter can lead to serious distortions in research results. At the same time, the lack of a worthy alternative explains the reasons for hushing up this serious problem. Here, we propose low-cytotoxicity encapsulated forms of cyanine 3.5 and cyanine 5.5, enabling intracellular uptake and facilitating single-cell labeling and tracking as an efficient alternative to existing staining. Only 16.9% of myoblasts (C2C12) exchanged encapsulated dyes compared with 99.7% of cells that exchanged the free form of the same dyes. Simultaneous application of several encapsulated cyanine dyes, combined with the possibility of photoconversion, provides multi-color coding of individual cells. Encapsulation of cyanine dyes allows reliable labeling and reduces the transfer of the dyes between cells.