Regional bio-optical algorithms for SeaWiFS and MERIS over the Alboran Sea are retrieved by computational inversion of an ocean colour model. The input to the model is a set of in situ measurements of the water constituents from the OMEGA Project. The algorithms for the estimation of phytoplankton chlorophyll and dissolved organic matter are robust with respect to the variation of the internal parameters of the model. The regional chlorophyll algorithm for SeaWiFS is compared to the global one used by NASA, and an example of the application of the chlorophyll and yellow substance algorithms to SeaWiFS imagery over the study area is shown and discussed.