Changes in phytoplankton assemblages may significantly alter elemental cycles. However, the differing contributions of phytoplankton functional types to the biological pumps have not been explored. This study aims to evaluate the sinking process of phytoplankton to the bathypelagic layer at the functional-type level. We collected sinking particles using sediment traps moored at 387 m and 890 m depths from June to August 2022 in the Sea of Japan and morphologically divided them into aggregates and fecal pellets (ellipsoidal, cylindrical, spherical, and tabular). The carbon flux of sinking particle types was measured, and the phytoplankton assemblages in every sinking particle type were investigated with 16S rRNA gene amplicon sequencing. The proportion of the phytoplankton-origin amplicon sequence variant (ASV) per total 16S gene sequence reads numbers in aggregates was 5.76 ± 0.496% (median ± interquartile range, n = 6) at 890 m, which was significantly lower than that in the ellipsoidal fecal pellets (8.96 ± 6.00%, n = 64) at 890 m depth. The number and sizes of the ellipsoidal pellets, considered appendicularian-origin, significantly increased with depth, and bigger ellipsoidal pellets were richer in phytoplankton ASVs. Diatom Chaetocerotales were the dominant phytoplankton group in each sample type and depth, except in the ellipsoidal and cylindrical fecal pellets at 890 m depth, where cyanobacteria Synechococcus was dominant. This suggests that phytoplankton, including Synechococcus, is effectively transported to the bathypelagic layer via the mesopelagic appendicularians repackaging process, while diatom Chaetocerotales effectively sink, regardless of the sinking processes.