Occurrence of cassava mosaic begomoviruses in national cassava germplasm preserved in two agroecological zones of Côte d’Ivoire Abstract Cassava production in Côte d’Ivoire is hampered by cassava mosaic disease (CMD) which is caused by several begomovirus species. To increase cassava production and conserve genetic resources, the Centre National de Recherche Agronomique (CNRA) maintains a germplasm collection of 610 cassava accessions of various origins. We carried out an epidemiological assessment of the collection and a molecular characterization of the viruses infecting CNRA cassava germplasm which is maintained in open fields in Bouaké and Man. The field in Man was less affected (incidence: 49.78%, severity: 2.23, whitefly infection: 2.23%) by CMD despite the abundant whitefly populations (1.34 per plant) observed, compared to Bouaké (incidence: 74.54% , severity: 2.92, whitefly infection: 8.04% and whitefly population of 0.34 per plant). However, the predominant mode of CMD transmission was through infected cassava cuttings in both sites. PCR analysis showed that the East African cassava mosaic Cameroon virus (EACMCMV) was always found in co-infection with African cassava mosaic virus (ACMV) which also occurred in single infection. Co-infections of EACMCMV and ACMV were prevalent in Bouaké (52.64%) compared to Man (13.87%). Eleven complete genome sequences of cassava mosaic begomoviruses infecting the CNRA germplasm were obtained, and phylogenetic analysis showed that they are closely related to ACMV and EACMCMV isolates from Ghana, Burkina Faso, and Nigeria. The results of the study will assist breeders to accurately screen progeny resulting from parental lines for CMV resistance, enabling the strategic distribution of new clean cassava planting materials to reduce the impact of CMD.