A new, simple and sensitive method for determining and confirming methylene blue and its analogues such as azure A, azure B, azure C, thionine, and new methylene blue in fish muscles have been developed. The method is based on acetonitrile extraction followed by extract purification using dispersive solid-phase extraction (dSPE) with basic aluminium oxide (ALN) and solid-phase extraction (SPE) using primary and secondary amines (PSA) sorbent in matrix adsorption mode. The separation and detection of the dyes in the fish extract are achieved within 5 min by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) using an octadecyl analytical column with a mixture of acetonitrile, methanol and 0.1% formic acid as a mobile phase in gradient elution. The developed method has been in-house validated according to European law. The method recovery for fish muscle was 98.3–103.1%, whereas the decision limit (CCα) was from 0.45 to 0.49 µg kg−1.