Objective To investigate three cases of food poisoning caused by the toxic mushroom in Nanping, Fujian Province in 2017, accumulate the experience and solutions for the investigation and disposal of wild mushroom poisoning and help to reduce the morbidity and mortality caused by food poisoning incident in the future. Methods Review the clinical treatment data of the patients with poisoning, and identify the species of the mushroom samples by internal transcribed spacer (ITS) barcode identification technology. Results The epidemiological investigation, clinical characteristics analysis and ITS sequencing verification were carried out for three poisoning incidents at the end of August 2017 with 17 poisoning patients and 3 deaths. According to the result of the epidemiological characteristics of poisoning, the clinical characteristics of the poisoning patients, the changes of biochemical indexes and the identification result by molecular biology, two cases of food poisoning were confirmed to be caused by Russula subnigricans Hongo and another case was presumed to be caused by this toxic mushroom. Conclusion The molecular biology identification was firstly used to identify 2 cases of mushroom poisoning incidents owing to Russula subnigricans Hongo in Fujian Province, which is widely distributed among the mountainous areas in Fujian Province.