High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbour a unique genomic repertoire, but their composition and diversity are largely unknown. Here we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (???4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. OTUs composition was significantly different among lakes and between seasons. Members of the class Opitutae, Spartobacteria, Burkholderiales, and Actinobacteria were dominant, but only the hgcI clade (Actinobacteria) and the Comamonadaceae family (Burkholderiales) were shared between seasons among the three lakes. In general, a large percentage (up to 42%) of the rare OTUs was unclassified even at the family level. In one lake, a pycnocline and an anoxic water layer with high abundance of Thiocapsa sp. was found in the wet season indicating that the known polymictic thermal condition is not always given. Our study highlights the particular BCC of tropical high-elevation lakes and also how little is known about the variability in physico-chemical conditions of these ecosystems.