As an important endogenous biothiol, cysteine is involved in various physiological processes. Besides, cysteine also plays an important role in the regulation of intracellular redox levels and the synthesis of bioactive substances. Cellular organelles all act an essential role in the life process, but different cellular organelles have their own unique functions, which makes the mechanism of cysteine in different organelles may be different. The high sensitivity and in situ analyze ability of fluorescent probes provide a method to monitor cysteine in different organelles, which is helpful to understand the mechanism of cysteine in physiological process more comprehensively. In this review, the recent reports on cysteine specific fluorescent probes are classified according to their targeted organelles. Besides, the property of those probes, including their structure, response mechanism, spectral properties and biological applications, is summarized.