Esca and Black Dead Arm (BDA) are two major actors of grapevine trunk decline diseases that affect worldwide. The knowledge about the symptoms of these diseases and the microflora associated with these wood pathologies is still incomplete in Tunisia, although they begin to cause considerable damage in our vineyards. In order to better characterize the microflora colonizing the trunk of vine, samples were collected from eight vineyards in the north of Tunisia. Symptoms were described and isolates taken at the level of sick and healthy vines. A halophilic bacterium J9 was used as antagonistic agent and has been tested against fungi isolated. Two symptoms were observed: rapid total or partial drying resulting in the death of the cep (apoplectic form of esca) and the presence, under the bark of the trunk of an orange to brown band, characteristic of the Black Dead Arm Disease (BDA). For the varieties studied, cultivated and diverse microflora are colonizing the vines. Many saprophytic fungi such as Aspergillus spp and Alternaria alternata were detected in the healthy wood and at the level of necrosis. The identification of fungi by molecular methods including by PCR and sequencing showed the presence of Phomopsis viticola and Diplodia seriata, two pathogens described in the literature as involved in diseases of wood. Next to these pathogens, the molecular analysis confirmed the presence of Alternaria alternata as majority saprophyte in healthy and diseased wood. The use of bacterial antagonist gave pretty promising results especially with Diplodia seriata. This is the first report of Phomopsis viticola and Diplodia seriata infections of grapevines in Tunisia.