Fusarium head blight and Fusarium crown rot are two important fungal diseases of wheat worldwide. This research was carried out to study the most important species associated to these two diseases in Algeria. Symptomatic crowns and heads were collected from different wheat growing regions in Algeria. Morphological and molecular identifications showed the occurrence of six fungal species isolated from crowns for the 2 years: Fusarium culmorum (68%), F. pseudograminearum (10%), F. verticillioides (3%), F. avenaceum (2%), Microdochium majus (13%) and M. nivale (4%). Two species only, F. culmorum (94.1%) and F. pseudograminearum (5.9%), were obtained from the heads. Among the Fusarium spp., 30 isolates were chosen for the pathogenicity tests: F. culmorum isolated from symptomatic crowns (n = 10), F. culmorum isolated from blighted heads (n = 10) and F. pseudograminearum (n = 10). Pathogenicity tests were carried out by using three different methods: seed inoculation, soil inoculation and head inoculation. Results showed that F. culmorum isolates were the most aggressive on the wheat seedlings and on the head. However, F. pseudograminearum isolates were the most aggressive on the crown. High correlations were found between Fusarium isolates aggressiveness on the wheat seedlings and on the head for the two F. culmorum groups (FCC: r = 0.89 and FCH: r = 0.85). These results provide a simple in vitro test to predict pathogenicity of the F. culmorum isolates for head blight. This study highlight that F. culmorum is the dominant species associated with FHB and FCR in Algeria. Also, this is the first report concerning the identification of F. pseudograminearum, M. majus, F. verticillioides and F. avenaceum from wheat in Algeria.