Abstract:[Background] In recent years, Huanglong travertine landscape has seen large-scale growth of algal mats with thickness of 3–5 cm, posing a threat to the travertine deposition and affecting the ornamental value of the landscape. [Objective] To dissect the structure of the algal mats and the reasons for the large-scale growth, thereby to control the growth of algae, and to propose management methods. [Methods] The composition of eukaryotic species in different layers of typical epiphytic algal mats in the Huanglong travertine area was analyzed based on PE-250. Their morphology was characterized via the field emission scanning electron microscope, and the correlation between the thickness of algal mats and water environment parameters was examined. [Results] The algal mats were home to about 400 species of eukaryotes, with the dominant algae of Diatomea (mainly Cymbella), Rotifera, and Streptophyta. Non-metric multidimensional scaling (NMDS) analysis and clustering analysis showed that the composition of eukaryotic species in the middle layer of the algal mats was highly similar to that in the lower layer. Diatoms dominated the upper layer, and the middle layer was mainly composed of filamentous algae. For the lower layer, travertine particles were seen in the reticular structure composed of filamentous algae. The thickness of algal mats was mainly in positive correlation with the total nitrogen (TN), total phosphorus (TP), and dissolved oxygen (DO) in the water (p<0.05). [Conclusion] The algal mats boast abundant species in a few phyla. The three layers of the mat are distinct from each other in species composition and microstructure and water eutrophication can explain the rapid growth of algal mats. This study lays a theoretical basis for the management of algal blooms in Huanglong Scenic and Historic Interest Area.