A ship-board surface flow through system was equipped with a WET Labs ac9 configured with a switchable 0.2 mm filter cartridge to measure total and filtered absorption and attenuation. The filter was engaged routinely throughout each day. Observations were collected on two cruises (September 2005 and January 2006) along an equatorial transect from approximately 8N to 8S along the 140W longitude then east to 125W and from 8S to 8N, completing 3 sides of a box. Discrete samples were collected from the flow through system and processed for spectrophotometric particulate absorption coefficients. The in situ absorption coefficients were of the order 0.005 to 0.01 m-1, the same order as the resolution of the ac9. In these optically clear waters, instrument stability and calibration are of utmost importance for retrieving accurate absorption spectra. We experienced problems with instrument stability on one cruise and were plagued by pure water calibration issues on both. However, by computing the particulate absorption and attenuation spectra from the difference between temporally adjacent total and filtered water observations we were able to retrieve robust and accurate spectra, which compared well with those derived from filter pad absorption observations, on highly resolved spatial scales. We are able to quantify seasonal and spatial variations in particle optical properties across the equatorial upwelling zone. The particle absorption is dominated by phytoplankton exhibiting spectral shapes consistent with small cell sizes and high light acclimation. The particle attenuation spectra are likewise consistent with small particle sizes. Particle backscattering ratios were derived from backscatter determined with a WET Labs ECOVSF sensor and total scatter calculated as the difference measured particle attenuation and absorption. Values were consistent with waters dominated by particles of low index of refraction.