Although scarce, available data suggest that the epidemiology of invasive aspergillosis (IA) in North Africa differs from northern countries, where more than 80 % is caused by Aspergillus fumigatus. This study aimed at describing the epidemiology of IA in the region of Sousse, Tunisia, and at assessing the usefulness of the available diagnostic tools. For 2 years, clinical and mycological data were prospectively collected from 175 neutropenia episodes of 91 patients hospitalised in the haematology department at the Farhat Hached hospital in Sousse (Tunisia). Screening for galactomannan antigen was positive in 40 % of neutropenia episodes; Aspergillus PCR was positive in 42 % of the tested sera. Nine patients were classified as probable and two as possible IA according to the EORTC/MSG criteria. Twelve patients who prematurely died, had no CT scan and could not be classified. Fifty-six Aspergillus spp. were isolated in 53 (6.5 %) sputa collected from 35 (20 %) patients. The following species were identified with MALDI-TOF mass spectrometry and DNA sequencing: A. niger, 35 %; A. flavus, 38 %; A. tubingensis, 19 %; A. fumigatus, 4 %; A. westerdijkiae, 2 % and A. ochraceus, 2 %. Our findings highlight the epidemiological features of IA in Tunisia, which is characterised by the predominance of Aspergillus spp. from sections Nigri and Flavi.