The formation of resting cysts is a strategy for survival in unfavorable environments by single cell organisms such as protists. Here, we show that Colpoda resting cysts have high salinity tolerance and investigate the changes in gene expression that underpin this effect. Colpoda resting cysts can tolerate saline conditions up to 3.5 % NaCl. A comparative transcriptome analysis of vegetative cells and resting cysts showed that the relative levels of expression of genes associated with membrane function increased in resting cysts. These changes in gene expression suggest that reconstruction of the plasma membrane is associated with salinity tolerance. The resting cyst forms cyst-specific cellular structure known as the cyst wall. The outer shell-like layer, called the ectocyst, while the inner multiple layers, known as the endocyst. The chemical analysis showed ectocyst contains chitin and endocyst contains several proteins. These structures can protect cells by acting as a biological armor or protective materials. The results of this study offer a possible scenario in which salinity tolerance enables the widespread dispersal of protists.