During 2008 and 2009, a new disease was noticed in eastern Sicily (Italy) in two re-grafted citrus orchards (Citrus sinensis (L.) Osbeck) on sour orange rootstock. Symptoms consisted of blight of vigorously growing shoots and a sooty canker on shoots and rootstock trunks. A Scytalidium-like fungus was isolated consistently from symptomatic tissues on 2% potato-dextrose agar (PDA). The mycelium was composed of branched, septate, brown hyphae which disarticulated into 0-1-septate phragmospores. In culture it also produced a pycnidial synanamorph, with hyaline conidiogenous cells that were intermingled with paraphyses. Conidia were ellipsoid to ovoid, hyaline, with an acutely rounded apex, truncate base, initially aseptate, becoming brown and 2-septate at maturity, with the central cell darker than the end cells. Genomic DNA was extracted from mycelia of single-conidial isolates cultivated on 2% malt extract agar and the nuclear rRNA operon spanning the 3’ end of 18S rRNA gene, the internal transcribed spacers, the 5.8S rRNA gene, and a part of the 5’ end of the 28S rRNA gene was amplified and sequenced. On the basis of morphological characters and molecular data, the fungal isolates were identified as Neoscytalidium dimidiatum (Penz.) Crous & Slippers. Koch’s postulates were satisfied and confirmed the pathogenicity of the fungus. N. dimidiatum appears to pose a serious threat to re-grafted citrus orchards.