From midsummer to fall, cyanobacterial harmful algal blooms (cHABs) producing microcystins (MCs), a class of hepatotoxic cyclic heptapeptides, plague Lake Erie's western basin. Since MC congener toxicities vary over 2 orders of magnitude, identification and characterization of the microcystin congener profile can be crucial information when balancing between public health and local economic resilience. Herein, five hydroxyproline (Hyp)-containing MCs were discovered in a Lake Erie cHAB. High-resolution liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS), tandem mass spectrometry (MS/MS), and thiol derivatization were used in the putative identification of novel MC congeners. Among the five novel congeners, MC-LHyp, MC-HpeHyp, [Dhb]MC-HilHyp, and [Dhb]MC-YHyp contained single Hyp at position 4 of the cyclic structure, while MC-HypHyp contained two Hyp residues at positions 2 and 4 of the cyclic structure. The hydroxyproline amino acid imparts a more rigid peptide backbone because it forms a ring by bonding back to the amino group. Hence, the toxicities of Hyp-containing MCs and their isomers need to be elucidated. Furthermore, the discovery of hydroxyproline-containing MCs stresses the importance of understanding the genetic and environmental mechanisms of MC biosynthesis.