High-mountain lakes (HMLs) are remote, extreme, and sensitive ecosystems recognized as sentinels of global change. Lakes El Sol and La Luna are very close to each other inside the crater of the Nevado de Toluca volcano, but they differ morphometrically and limnologically. This study aimed to identify the seasonal fluctuation of the phytoplankton communities of these two tropical HMLs. El Sol phytoplankton comprised 50 taxa (chlorophytes, diatoms, charophytes) and La Luna 28 taxa (diatoms, euglenoids). The abundance of phytoplankton in El Sol was three times higher than in La Luna, and the biomass in El Sol was five times higher than in La Luna. Tropical seasonality was reflected differently in each lake. In El Sol, the highest phytoplankton abundance occurred in the rainy season, while the highest biomass was recorded in the dry/warm season. Conversely, in La Luna, abundance and biomass were more prominent in the dry/cold season. The study found that no meteorological or limnological factors could explain the seasonal dynamics of the taxonomic richness, abundance, or biomass of the phytoplankton communities in both lakes. The differences between the lakes are likely due to the more extreme conditions of La Luna, such as lower pH, ultra-oligotrophy, and increased exposure to ultraviolet radiation (UVR). Additionally, the introduction of rainbow trout into El Sol in the 1950s may have also contributed to the differences.