Azerbaijan is one of the most ancient centers of grape cultivation. The presence here of plenty of local high-quality varieties is a result of long selection. The ancient monuments found out during archeological excavations and also numerous literary data testify to an antiquity of grapevine cultivation in Azerbaijan. Under the influence of spontaneous national selection during centuries, the set of grape varieties and forms which demanded studying, economic valuation, botanical description and classification has been created. This distribution is almost conditional because there are also the pests in partially infected and a few infected regions (free zones). It is enough to mark the fact that phylloxera was found in just 9 hectares of grape plantations, but now about 50-60% of plantations are infected with phylloxera (1). The samples of grape varieties (Kaberne, Tabrizi and Bayanshira) which have been infected with phylloxera have been taken from viticulture plantations of Gazakh region with the purpose of determination of species’ composition of microorganisms which are the cause of rotting the roots of grapevines in Azerbaijan conditions. The separation from roots of grape and reproduction of phytopathogen and saprotrophic root rotting microorganisms which cause rot of grapevines infected with phylloxera is carried out according to the method proposed by P.N.Nedov (2, 3) with the purpose of creating complex artificial infection background.  Root samples from infected by phylloxera grape varieties Kaberne, Tabrizi and Bayanshira collected from farms of Gazakh region were analyzed and species composition of microorganisms, which cause the second pathologic process – rotting, was determined.  The quantity of microorganisms separated from the roots of Kaberne grape varieties infected by phylloxera has been 100 %. From these, it has been identified that the funguses belonging to Cylindrocarpon species are 30%, but in the roots of this grape variety, it hasn’t been discovered any fungus belonging to Gliocladium and Fusarium species. The bacteria that belong to phytopatogenic Pseudomonas species – 28.5%, the bacteria that belong to Bacillus species – 17.5% were identified. At the same time, it has been identified that here are funguses belonging to saprotrophic Mucor species – 10.5%, the funguses belonging to Absidia species – 9%, the funguses belonging to Rhacodiella species – 4.5%. The quantity of microorganisms separated from the roots of Tabrizi grape varieties infected by phylloxera have been 100 %. From these, it has been identified that the funguses belonging to phytopatogenic Gliocladium species are 11.5%, the funguses belonging to Fusarium species are 25%. In the roots of this grape variety, it hasn’t been discovered any fungus belonging to Cylindrocarpon species. There were identified bacteria belonging to phytopatogenic Pseudomanas species – 18 %, the bacteria belonging to Bacillus species – 35%. In the roots of this grape variety, it hasn’t been discovered any fungus belonging to saprotrophic species. The quantity of microorganisms separated from the roots of Bayanshira grape varieties damaged by phylloxera have been 100%. From these, it has been identified that funguses belonging to phytopatogenic Gliocladium species are 30.5%, funguses belonging to Cylindrocarpon species – 31%, the funguses belonging to Fusarium species – 13.5%. In the roots of this grape variety aren’t discovered bacteria. As well as is identified that there are the funguses belonging to saprotrophic Penicillium species – 10%, the funguses belonging to Absidia species –7.5%, the fungi belonging to Rhacodiella species –7,5%.