Fig mosaic disease (FMD) is a viral disease that spreads in all Tunisian fig (Ficus carica L.) orchards. RT-PCR technique was applied to leaf samples of 29 fig accessions of 15 fig varieties from the fig germplasm collection of High Agronomic Institute (I.S.A) of Chatt-Mariem, to detect viruses associated to FMD. Analysis results show that 65.5% of the accessions (19/29) and 80.0% (12/15) of the fig varieties are infected by FMD-associated viruses. From all fig accessions, 41.4% of them are with single infection (one virus) and 24.1% are with multi-infections (2 virus and more). Viruses infecting fig leaf samples are Fig mosaic virus (FMV) (20.7%), Fig milde-mottle-associated virus (FMMaV) (17.25%), Fig fleck associated virus (FFkaV) (3.45%), and Fig cryptic virus (FCV) (55.17%). A reliable protocol for FCV and FMMaV elimination from 4 local fig varieties Zidi (ZDI), Soltani (SNI), Bither Abiadh (BA), and Assafri (ASF) via in vitro culture of 3 meristem sizes was established and optimized. With this protocol, global sanitation rates of 79.46%, 65.55%, 68.75%, and 70.83% respectively for ZDI, SNI, BA, and ASF are achieved. For all sanitized varieties, the effectiveness of meristem culture for the elimination of FCV and FMMaV viruses was related to meristem size. Meristem size 0.5 mm provides the highest sanitation rates ranging from 70% to 90%.