Viral nervous necrosis virus (VNNV) is the aetiological agent of viral nervous necrosis (VNN), a widespread disease affecting different marine and freshwater fish species. Striped jack nervous necrosis virus (SJNNV) and red-spotted grouper nervous necrosis virus (RGNNV) are the only genotypes of the Betanodavirus genus recorded in the Iberian Peninsula to date, but a high percentage of wild specimens simultaneously carrying both genotypes has been recently reported. The coexistence of the two viruses may affect the course of both viral infections. In the present study, viral genome quantification by two absolute real-time PCR protocols has been performed to characterise the effect of the RGNNV-SJNNV coexistence (coinfection and superinfection) on the replication of each genotype in E-11 cells. This is the first study showing the effect of the coexistence on the viral replication of two genotypes within the Betanodavirus genus. The results obtained in vitro showed the partial inhibition of SJNNV replication by the coexistence with RGNNV, whereas RGNNV replication was favoured in coinfection or superinfection with SJNNV.