Ocean surface waters are expected to warm by 2–6 °C over the course of this century as a result of climatic change. We aim to assess the viral abundance and dynamics of viral lytic-lysogenic replication strategies in coastal waters in Taiwan and Japan during the winter of 2023. In particular, we examine both changes in lytic and lysogenic viral production as a function of warming. In this study, in situ temperature treatments with mitomycin C induced lower bacterial growth rates of 0.003 to 0.033 h⁻¹ than control treatments of 0.031 to 0.064 h⁻¹. Furthermore, bacterial growth rate without mitomycin C under warmed condition increased between 0.040 to 0.093 h⁻¹. There was a wide range of inducible prophage detected, ranging from undetectable to 14.2%. There was a higher rate of lysogenic infection under warmed conditions at all stations, ranging from 14.6 to 41.8%. Based on the observations that lysogeny occurs at warm treatments and increases with increased bacterial production, we suggest that there is a decrease in the amount of carbon entering the dissolved phase through viral shunts (lysed bacteria), favoring the microbial loop (grazing on bacteria).