Scab caused by the fungus Fusicladium eriobotryae is the most serious disease affecting loquat in Spain. Isolation of F. eriobotryae from infected tissue on culture media can be difficult due to its slow growth. A polymerase chain reaction (PCR) based protocol was developed for F. eriobotryae-specific identification from pure culture or infected loquat tissues. The primer set was designed in the elongation factor 1-α gene (EF1-α), and specificity and sensitivity for single and nested-PCR were validated. The nested-PCR assay resulted in 100% positive detection of F. eriobotryae in naturally and artificially infected tissues. This protocol can be useful for routine diagnosis, disease monitoring programs and epidemiological research.