This document specifies the general principle and the technical protocol for the validation of identification methods of microorganisms for microbiology in the food chain. As there is no reference method, this document provides a protocol to evaluate the performance characteristics and validate the method workflow using well-defined strains. When required, an additional identification method can be used. This document is applicable to the validation of identification methods of microorganisms that are used for the analysis of microorganisms in: products intended for human consumption; products for feeding animals; environmental samples in the area of food and feed production and handling; samples from the primary production stage. Validated identification methods cannot be used instead of confirmation described in: the reference method; an alternative method validated in accordance with ISO 16140-2; an alternative method validated in accordance with ISO 16140-6. In these instances, the identification method shall be validated in accordance with the ISO 16140-6 to be used as a confirmation method. This document is, in particular, applicable to bacteria and fungi. Some clauses can be applicable to other (micro)organisms, to be determined on a case-by-case basis.