Population-genomic analyses are essential to understanding factors shaping genomic variation and lineage-specific sequence constraints. The dearth of such analyses for unicellular eukaryotes prompted us to assess variation in Paramecium, one of the most well-studied ciliate genera. The aurelia complex consists of ~15 morphologically indistinguishable species that diverged subsequent to two rounds of whole-genome duplications (WGDs), as long as 320 MYA, and are well known for their streamlined genomes. We examine patterns of polymorphism by sequencing whole genomes of 10-12 worldwide isolates of each of three species belonging to the Paramecium aurelia complex: P. tetraurelia, P. biaurelia, P. sexuarelia, and two outgroup species that do not share the WGDs: P. caudatum and P. multimicronucleatum. An apparent absence of strong global geographic population structure suggests continuous or recent dispersal of Paramecium over long distances. Introns and intergenic regions are highly constrained relative to 4-fold degenerate sites, more so in species with smaller intergenic regions. Nuclear genome diversity is reduced up to ~100-150 bp both upstream and downstream of genes, suggesting the presence of densely packed regulatory modules. Comparison of sequence variation at non-synonymous and synonymous sites suggests similar recent selective pressures on paralogs within and orthologs across the deeply diverging species and allows identification of possible candidates of duplicate genes that might be undergoing non-functionalization. This study serves as a first attempt at a genome-wide population-genomic analysis in Paramecium, and provides a valuable resource for future studies in evolutionary and functional genetics in ciliates.