Automated image analysis was used to assess changes in the mesozooplankton community structure from the coastal upwelling zone off Central/southern Chile at Station 18 (36 degrees S). Nearly monthly samples from August 2002 to December 2005 were processed to obtain zooplankton size spectra in the size range of 0.25-30.25 mm and taxa classification. The slope of the log(2)-normalized size spectra (b), taxa richness (R) and the Shannon index of diversity (H') were chosen as community descriptors and related to oceanographic variables. Size spectra exhibited significant linear regressions and yielded slopes in the range of -0.25 and -1.76, whereas R ranged between 13 and 19. During the upwelling period (September to March), b, R and H' were significantly higher compared with the non-upwelling period (April to August). A principal component analysis showed that these descriptors were linked to depth of the oxygen minimum zone (OMZ), Ekman transport (Ek) and Salinity, the OMZ being the most strongly correlated. The shallow OMZ (< 20 m) constrains and aggregates plankton in the upper layer, causing: (i) a less steep size spectrum, because of appearance of large-sized classes, and (ii) increased diversity of either taxa or size classes, or both. Our findings suggest that input of zooplankton into the food-rich layer upon ascent of the OMZ may enhance carbon flux through the pelagic food web. Higher efficiency of transfer of primary production into fish production in coastal upwelling systems with a shallow OMZ system could thus be expected.