To investigate latitudinal variations in the zooplankton community along the meridian line ($5^{circ}N-12^{circ}N$, $131.5^{circ}W$), we measured temperature, salinity, nitrate, chlorophyll-a and zooplankton at depths above 200 m from July $10^{th}$ to $25^{th}$, 2003. For comparative analysis, data of the physico-chemical properties and chl-a were matched to the two sampling depths (surface mixed layer and thermocline depth-200 m) of zooplankton. Latitudinal differences in the mesozooplankton distribution were mainly influenced by divergence formed at a boundary line formed by currents of opposing directions, consisting of North Equatorial Current (NEC) and North Equatorial Counter Current (NECC). High concentrations of chl-a south of $9^{circ}N$, caused by equatorial upwelling related nutrients, is thought to be affected by the role of this divergence barrier, supported by relatively low concentrations in waters north of $9^{circ}N$. The latitudinal differences of the chl-a were significantly associated with the major groups of zooplankton, namely calanoid and cyclopoid copepods, appendicularians, ostracods, chaetognaths, invertebrate larvae, and others. And temperature significantly affected the latitudinal variation of radiolarians, siphonophores, salps and immature copepods. The latitudinal differences in the two factors, temperature and chl-a, which explained 71.0% of the total zooplankton variation, were characterized by the equatorial upwelling as well as the divergence at $9^{circ}N$. The physical characteristics also affected the community structure and abundance of zooplankton as well as average ratios of cyclopoid versus calanoid copepods. The abundance of dominant copepods, which were consistent with chl-a, were often associated with the carnivorous zooplankton chaetognaths, implying the relative importance of bottom-up regulation from physical properties to predatory zooplankton during the study period. These results suggested that latitudinal distribution of zooplankton is primarily controlled by current-related divergences, while biological processes are of secondary importance in the northeastern Equatorial Pacific during the study period in question.