The production of blueberry in Peru has been increasing over the last years. Dieback and stem blight of plants are the most prominent disease symptoms observed in blueberry orchards. This study evaluated the diversity and pathogenicity of Lasiodiplodia and Neopestalotiopsis species associated with dieback of blueberry plants in Peru. A collection of isolates was initially subjected to Microsatellite-primed PCR (MSP-PCR) fingerprinting and further characterised by sequence analyses of the rDNA internal transcribed spacer region (ITS), translation elongation factor 1-alpha (tef1-α) and β-tubulin (tub2). The phylogenetic analyses revealed the presence of Lasiodiplodia theobromae, L. laeliocattleyae and Neopestalotiopsis rosae. Lasiodiplodia laeliocattleyae and N. rosae are reported for the first time in blueberry plants associated with dieback and stem blight symptoms. Additionally, N. rosae is newly reported from Peru. Inoculation trials of blueberry plants confirmed the pathogenicity of Lasiodiplodia and Neopestalotiopsis species and revealed differences in aggressiveness among species and isolates.