Abstract: Since nanoflagellate grazing and viral lysis differ in their impact on the microbial food web, it is important to assess their relative importance on bacterial mortality fractions. This study investigated the abundance of microbial assemblages and the loss of bacteria due to viral lysis and nanoflagellate grazing at two different depths (3 and 135 m) in the coastal waters of subtropical western Pacific during summer (July, August, and September 2012). The bacterial growth rates in the surface waters varied from 0.07 to 0.09 h−1, a range higher than those found in the deep waters (0.013 to 0.016 h−1). The grazing rates of nanoflagellates on bacteria ranged from 0.051 to 0.058 h−1 and from 0 to 0.004 h−1 in the surface and deep waters, respectively. During the study period, nanoflagellate grazing was responsible for most of bacterial mortality (81–87 %) relative to viral lysis in the surface waters, while viral lysis was responsible for 67–75 % of the total bacterial mortality in the deep waters.