The Ecuadorian Tropical Andes serve as vital biodiversity hotspots, crucial for hosting and preserving unique endemic species. While numerous taxonomic groups within these hotspots have been extensively studied, microalgae remain relatively unknown. This study aimed to document the microalgal diversity of Tropical Andean lakes in Ecuador and its relationship with abiotic environmental factors. Water samples were collected from 28 lakes throughout 10 conservation areas, spanning different altitudes in the Ecuadorian Tropical Andes, along with water physical/chemical data. A total of 92 microalgal genera were identified, spanning Bacillariophyta, Chlorophyta, Glaucophyta, Ocrophyta, Cyanophyta, and Euglenophyta. Lakes such as Rodeococha, Anteojos, Chinchillas, Toreadora, Magdalena, and La Mica exhibited the highest richness of microalgal genera. A positive association between temperature and the majority of microalgal phyla, except Glaucophyta, was observed. On the other hand, negative correlations were observed between total dissolved solids and water conductivity with microalgal biodiversity. Additionally, all groups displayed negative associations with pH, except Glaucophyta. The Jaccard similarity index was low among lake communities in agreement with the uniqueness of genera found in some lakes. This study represents a fundamental baseline for future investigations into Ecuador’s microalgal diversity and its relationship with abiotic environmental factors in the delicate freshwater ecosystems of Tropical Andean lakes.
