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Monthly phytoplankton samples were collected from January 2013 to December 2015 at a fixed sampling site in Bahía de La Paz, Gulf of California. During this study 26 samplings were Amphidinium cf. carterae positive. The highest densities of A. cf. carterae (754.2 × 103 to 1022.4 × 103 cells L−1) were recorded during a bloom detected in January 2015 when water temperatures were 20–22 °C. This dinoflagellate showed a well-marked seasonal variation, being found mainly from November to April. Blooms of the species were linked to the upwelled water due to the northwesterly wind. Cysts surrounded by a mucilaginous membrane of A. cf. carterae were found. We also observed these hyaline cysts inside zooplankton fecal pellets. Other benthic/tychoplanktonic dinoflagellates and diatoms, including some potentially toxic species were also found. The occurrence of blooms of A. cf. carterae in Bahía de La Paz could represent a risk for aquaculture activities and human health. • Amphidinium cf. carterae is a potentially toxic dinoflagellate in Mexican waters. • Its highest densities (1022.4 × 103 cells L−1) were recorded in January 2015. • Blooms of Amphidinium cf. carterae in Bahía de La Paz were found at 22 °C. • Blooms of the species are linked to the upwelled water due to the northwestern wind. • No apparent detrimental effects on the marine fauna were observed during the blooms. [ABSTRACT FROM AUTHOR]