Understanding mutation rate evolution is essential for elucidating evolutionary processes. To date, spontaneous mutation rates have been estimated in approximately 200 species, predominantly animals, plants, green algae, and bacteria. However, both mutation rates and spectra vary widely across the tree of life, and studies on new model species have recently provided valuable insights into the evolution of mutation rates. Here, we estimate the spontaneous mutation rate and spectrum in the glaucophyte Cyanophora paradoxa through a mutation accumulation experiment. While it's µ_bs of 2×^-10 mutations per site per generation is a typical value for a unicellular species, C. paradoxa exhibits highest insertion-deletion rate measured to date (µ_id = 2×^-9). This high µ_id is primarily driven by insertions in intergenic regions located within or adjacent to palindromes, inverted repeats (IR), or direct repeats (DR), sequence features known to promote noncanonical DNA structures and to act as mutation hotspots. Beyond its magnitude, the insertion spectrum displays a unique pattern of DR and double three nucleotides DR and IR repeats centered around CG nucleotides, likely generated by template switching and topoisomerase activity. This creates a positive feedback loop further amplifying the insertion rate of C. paradoxa. These results highlight C. paradoxa’s unique mutation patterns and position glaucophytes as key models for studying mutation processes.