This dataset contains the values of abundance of zooplankton collected along the west coast of Baja California on board the R/V BIPO INAPESCA within the Mexican Economic Exclusive Zone (EEZ) off the West Coast of Baja California Peninsula, between 32.5º to 23º N and 110º to 122º W covering 5173 nautical miles (nmi). The Bongo system (505-μm of mesh opening) with two cylindrical-conical nets (2 m in length and 71 cm of mouth diameter), each one fitted with a flexible cod end and a General Oceanics flowmeter at the mouth for the determination of the volume of water filtered was used to collect the zooplankton organisms from surface to 200 m depth. Diurnal and nocturnal samples were fixed in 4% formalin buffered with a saturated solution of sodium borate. Samples for taxonomic composition were sub-sampled when the total sample exceeded 20 ml, and at least two sub-samples of 10 ml were examined using a Carl Zeiss Stemi stereomicroscope (Horwood and Driver, 1976). The zooplankton organisms were identified to functional taxonomic groups and its abundance was standardized using the formula (N = n / Vf); where N is the standardized number of organisms in 1 m3; n is the number of organisms in the sample and Vf, is the volume of water filtered in each trawl.