This review discusses the use of fluorescent probes for identifying, isolating, and monitoring cells and organelles. Fluorescent probes have advantages over antibodies in live‐cell staining due to their small size and ability to penetrate the cellular membrane without fixatives or permeabilizers. However, different cell types exhibit different staining mechanisms based on their genetic profiles and the composition of proteins, enzymes, and lipids. The authors introduce a gating‐oriented live‐cell distinction mechanism where membrane transporters such as solute carriers and ATP are responsible for importing and exporting fluorescent probes. The mechanism for known and unknown transporter identification is elucidated through dose‐dependency, inhibitor tests, and genetic techniques such as clustered regularly interspaced short palindromic repeat modulation and screening. This review provides insights into cellular staining and its potential for understanding the gene profile of different cell types, as well as guiding the identification of membrane transporters.