Malachite Green (MG), a cationic triphenylmethane dye, has adverse effects on the immune and reproductive system. Thus, it is essential to develop a rapid, sensitive and high-selective method for determination of MG. Black phosphorus (BP) has high charge-carrier mobility (∼1000 cm V s) and high adsorption capacity for cationic dyes (i.e. MG) through both electrostatic and hydrophobic interactions. Thus, it potentially plays as a high-sensitive sensing platform for detecting MG. However, BP degrades within 12 h under humid condition, which limits its applications. To overcome this issue, cysteine (CYS) is used for protecting BP from oxidation and ceasing its degradation. To the best of our knowledge, it is the first time that CYS is used to functionalize BP, and a silicon interdigital electrode is fabricated with the functionalized BP and aptamer. The BP-based interdigital electrode shows a lowest detection limit of 0.3 ng L toward MG. This work provides a new route to prepare a large scale and selective biosensor for MG monitoring on site in future.