Recently, 24 sections were characterised in the genus of Alternaria. In this work, 27 isolates of Alternaria belonging to section Alternaria were isolated from different sources in Qena governorate, Egypt. The collected strains were identified using multi-locus products of internal transcribed spacer (ITS) region, small subunit (SSU), large subunit (LSU) and Alt a1 gene. Based on four loci, the phylogenetic analysis revealed that 26 isolates (96.3% of total isolates) identified as A. alternata and the last one isolate (3.7%) as A. arborescens. The different strains of Alternaria exhibited enzymatic variability ranged from 0.1 ± 0.07–2.3 ± 0.13U/ml for cellulase and 0.6 ± 0.20–3.7 ± 0.47 U/ml (pectinase). Within A. alternata isolates, biochemical properties (Cellulase and pectinase) did not correlate either to phylogenetic analysis or strain origin.