The diversity, co-occurrence patterns, and assembly processes of microeukaryotes in Antarctic freshwater lakes are not well understood, despite its wide distribution and ecological importance. This study used Illumina high-throughput sequencing to explore five freshwater lakes' microeukaryotic communities on the Fildes Peninsula during three summer seasons. A total of 33 phyla were detected, with the phytoplankton occupying the highest percentage of sequences (accounting for up to 98 %). Meanwhile, the main dominant taxa were Chrysophyta, Chlorophyta, and Cryptophyta. Alpha diversity varied among lakes, with Changhu (CH), Kitec (KT) lake having higher values, and Yue Ya (YY) lake having the lowest value. There were significant differences in microeukaryotic communities between lakes, with spatial and temporal variation in the relative abundance of dominant taxa (P