The East Sulu Sea, the area off the coast of the Zamboanga peninsula, is one of the major fishing grounds for sardine in the Philippines principally driven by primary production that follows seasonal upwelling in the area. Chaetognaths are zooplankton predators whose abundances may serve as control to overall plankton biomass in such productive waters. This study aims to compare and characterize chaetognath assemblages associated with structural attributes between high and low production areas within an upwelling area. Zooplankton were collected in February 2013 during an upwelling season using a 45cm-diameter NORPAC net with a 200um mesh bag attached to it. Three depth intervals (0-65m, 65-135m and 135-200m) were examined in each station for the vertical profiling of zooplankton. The mean zooplankton biomass for the high (Stn 24) and low (Stn 22) production stations were 51.8 ml 100m-3 and 75.8 ml 100m-3, respectively. A total of 993 chaetognaths with an average density of 47.5 ind. m-3 were collected from the Stn 24, and only 334 individuals accounting for an average density of 10.6 ind. m-3 from the Stn 22. The results show an aggregation of chaetognaths in the surface layer of the two stations, particularly in the high production station, contributing 80.96 ind. m-3 to the total zooplankton. Flacisagitta enflata was the most dominant species found in both stations. This study suggests that physical and biological controls may dictate chaetognath assemblage composition and distribution.