Picophytoplankton (0.2-3.0 μm), composed of prokaryotes such as Synechococcus (Syn), Prochlorococcus (Pro), and picoeukaryotes (Picoeuk), are distributed ubiquitously in all types of waters of varying trophic states.Among picophytoplankton, Syn is ubiquitous in both oligo- and meso-trophic oceanic and coastal areas; Pro has been found to be more abundant in oligotrophic waters than in eutrophic waters; Picoeuk are generally less abundant, although they can be large contributors to biomass and production. Picophytoplankton assemblages are the major contributors to primary production and organic carbon, and form the base of complex microbial food webs. The small picophytoplankton have a competitive growth advantage, especially in oligotrophic waters, because of their higher surface to volume ratios. In recent years, picophytoplankton in the southern South China Sea (SCS) have received increasing attention, as they account for the majority of primary productivity in this water. The picophytoplankton in SCS open areas are dominated by Pro, Syn, and Picoeuk. The majority of studies of picophytoplankton dynamics in the SCS have been biological investigations investigating chlorophyll a (Chl a), phytoplankton productivity, blooms, and community structure; however, information about the distribution of the picophytoplankton community and its driving factors, especially mesoscale eddy, are relatively scarce. In this study, we investigated the wintertime spatial distribution of picophytoplankton groups along the 113°E meridian in the southern SCS in 2011 using flow cytometry, and discussed the relationship between picophytoplankton distribution and environmental factors. The results showed that the depth-integrated abundances of Pro, Syn, and Picoeuk were(1.71 ± 0.47) × 10⁴, (1.50 ± 0.72) × 10³and (1.30 ± 0.50) × 10² cells/mL, and Pro abundance was 1 and 2 orders of magnitude higher than Syn and Picoeuk, respectively. Three types of picophytoplankton showed different distribution patterns, Pro dominated the upper 100 m, Syn dominated the upper 75 m and peaked in the 25 m layer; Picoeuk was mainly distributed in the upper 100 m and formed a subsurface maximum layer of 25 to 75 m, similar to the subsurface Chl a maximum layer. Between 9 and 11°N, the maximum layers of Pro and Syn were up-shifted, making their maximal values significantly lower than the surrounding water, potentially as a result of the upwelling induced by a mesoscale cold eddy; Picoeuk appeared at a subsurface maximum value with a higher abundance than the surrounding water, between 11 and 13°N, which was possibly caused by downwelling and induced by a mesoscale warm eddy. In addition, our results showed that Pro, Syn, and Picoeuk carbon biomass accounted for 59.16%±13.74%, 23.86%±10.83%, and 16.97%±5.51% of the total picophytoplankton carbon biomass, indicating that Pro was the main contributor to carbon biomass in this area. In addition, a correlation analysis showed that there was a positive correlation between Syn abundance and temperature, indicated that the higher temperature favored the growth of Syn; meanwhile, Syn abundance was negatively correlated with salinity, which might be caused by land-derived runoffs from the Menkong River, which often lowered salinity but increased nutrient levels. Picoeuk was significantly negatively correlated with nitrate and phosphate, indicating the presence of complicated inter-effects with other environmental factors. The response of picophytoplankton population distribution to mesoscale cold and warm eddies is a subject requiring further research to elucidate fully.