The subclass Peritrichia encompasses over 1,000 species of ciliates, demonstrating both wide distribution and significant morphological diversity across aquatic environments. Despite their ecological significance and unique biological attributes, genomic information for peritrichs has remained sparse. This study aimed to fill this gap by sequencing the genomes of seven distinct species of peritrich ciliates and employing advanced genomic technologies to investigate their metabolic characteristics, functional diversity and evolutionary relationships. Our analyses revealed a large number of genes annotated across various functional categories, with EggNOG annotations highlighting genes related to post-translational modification, translation and energy metabolism, suggesting a high adaptive and metabolic capacity. Notably, the diversity of CAZymes, particularly glycoside hydrolases, indicates metabolic complexity and the ability to degrade carbohydrates, critical for environmental adaptation and bacterial predation. Additionally, the presence of chitin-degrading enzymes in species like Trichodina acuta points to complex ecological interactions with hosts, with potential implications for natural ecosystems and commercial hatcheries. A concentration of glycosyl transferases found in the Vaginicolidae family suggests an enhanced capacity for glycoconjugate synthesis, possibly linked to lorica formation. The phylogenomic reconstruction was consistent with existing literature, uncovering intricate phylogenetic relationships. Overall, our findings significantly advance the understanding of peritrich ciliates by shedding light on their metabolic potential, ecological adaptability and evolutionary complexity, while also providing a genomic foundation for future ecological and evolutionary studies.