Proteins of all living cells undergo a myriad of posttranslational modifications (PTMs) that are critical to multifarious life processes. In this study, we describe the first comprehensive multiple PTM-omics atlas in parallel with quantitative proteome analyses of two representative species of trypanosomes, Trypanosoma brucei and T. evansi. Approximately 40,000 modified sites and 150 histone marks were identified in each species. Proteins involved in the redox system were mainly regulated in T. brucei, while proteins associated with motility were predominantly modified in T. evansi. The establishment of a database of multiple PTMs in the two parasites provides us with insight into the biological mechanisms that underpin life processes in trypanosomes with huge different life cycles.