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Priority Marine Regions (PMR) are important areas for biodiversity conservation in the Northwest Pacific Ocean in Mexico. The oceanographic dynamics of these regions are very important to understand their variability, generate analyses, and predict climate change trends by generating an adequate management of marine resources and their ecological characterization. Chlorophyll a (Chl a) is important to quantify phytoplankton biomass, consider the main basis of the trophic web in marine ecosystems, and determine the primary productivity levels and trends of change. The objective of this research is to analyze the oceanographic variability of 24 PMR through monthly 1-km satellite image resolution Chl a data from September 1997 to October 2018. A cluster analysis of Chl a data yielded 18 regions with clear seasonal variability in the Chl a concentration in the South-Californian Pacific (maximum values in spring-summer and minimum ones in autumn-winter) and Gulf of California (maximum values in winter-spring and minimum ones in summer-autumn). Significant differences (p < 0.05) were observed in Chl a concentration analyses for each one of the regions when climate patterns—El Niño/La Niña Southern Oscillation (ENSO) and normal events—were compared for all the seasons of the year (spring, summer, autumn, and winter). [ABSTRACT FROM AUTHOR]