Inflorescence rot is a devastating disease of date palm (Phoenix dactylifera L.) but has not been extensively characterised. Mauginiella scaettae Cav. 1925 (Pleosporales; Ascomycota), causal agent of this disease, was isolated from infected male and female inflorescences of date palm from different oases in the southeast of Algeria: Ouargla (strains OU1, OU2, OU3), Tougourt (strains TO1, TO2), Hadjira (strain HA), Oued (strains OE1, OE2), Ghardaia (strain GA) and Biskra (strain BI). Each strain of M. scaettae was used to infect healthy male inflorescence of date palms to satisfy Koch's postulates but follow on assessments were based on GA. Phylogenetic reconstruction using the rRNA sequence data (ITS and LSU regions) found no intraspecific differentiation of strains and confirmed the placement of M. scaettae within the family Phaeosphaeriaceae. Fourier Transform Infrared spectroscopy (FTIR) metabolite fingerprinting discriminated between fungal strains originating from male and female inflorescences. Scanning electron microscopy (SEM) characterisation of the infection processes for M. scaettae in both male and female inflorescences suggested a preference for stomatal entry. Our characterisation provides new insights into this inflorescence rot to allow better detection and management of the disease.