Faba bean samples with symptoms of yellowing, dwarfism, shoot proliferation, internode shortening, leaf sprouts and lack of pod and seed production were collected from Huancayo and Chupaca provinces, Junin-Peru, and analysed to verify phytoplasma presence and identity. After total nucleic acid extraction, the amplification with universal phytoplasma primers, using nested polymerase chain reactions, on the 16S ribosomal gene followed by restriction fragment length polymorphism analysis and sequence analysis allowed the classification of the detected phytoplasma in the subgroup 16SrIII-J. The alignment of 30 16S ribosomal gene sequences from 15 faba bean symptomatic samples from single plants allowed verifying the consistent presence of 5 single nucleotide polymorphisms that are however not modifying the phytoplasma classification. The phytoplasma identity was also corroborated by the amplification and the restriction fragment length polymorphism analyses carried out on the ribosomal protein gene amplicons obtained with primers specific for the phytoplasmas enclosed in the 16SrIII group. This is the first description in Peru of a disease associated with phytoplasmas in faba beans.