Dinoflagellates collected during red tide events in Bahia Mazatlan, Mexico during the early spring of 1999 and 2000 appeared under LM to belong to Prorocentrum mexicanum Osorio-Tafall. Observations with SEM of those populations showed marked differences in shape and microornamentation from the related species, Prorocentrum rhathymum Loeblich III, Sherley and Schmidt. In P. mexicanum, the presence and dimensions of poroids, the uneven distribution of trichocyst pores not located in depressions, and the general architecture of the periflagellar region are more closely related to Prorocentrum caribbaeum Faust. Also, P. mexicanum has a three-horned (sometimes two-horned) spine and is deeper in the anterior than the posterior region, whereas P. rhathymum has a simple small spine and its sagittal view is oval. Furthermore, the number and distribution of trichocyst pores in the periflagellar area is different between the two species, being located on both valves in P. mexicanum and only on the right valve in P. rhathymum. To date, true P. mexicanum has been described only from plankton sampling, whereas P. rhathymum was frequently mentioned associated with floating detritus (macroalgae) but also forming red tides. Altogether, the evidence presented demonstrates that P. mexicanum (planktonic) and P. rhathymum (epibenthic) are distinct species and are not synonyms, as is often accepted.