Unicellar, biomineralizing algae like diatoms or Synurales are ubiquitous in various habitats all over the world and have an outstanding role in different biogeochemical cycles. They are well known for their elaborate nanopatterned cell structures consisting of amorphous biosilica, which is intracellularly synthesized. Special biomolecules assist in the silica formation. In particular, species-specific long-chain polyamines (LCPAs) are commonly found in diatom biosilica and seem to play a special role due to their ability to self-assemble and induce silica precipitation. In contrast to diatoms, no species from the order Synurales have been tested yet for the presence of LCPAs. Therefore, the present work deals with the analysis of Synura echinulata biosilica using a novel HPLC-HR-MS/MS method. The presence of unique LCPAs is shown, and their structure is elucidated via MS/MS experiments. LCPAs from S. echinulata are based on amino butyl repeat units—in contrast to previously described LCPAs from other organisms, which are mostly based on amino propyl repeat units. The ubiquitous presence of LCPAs in biomineralizing species strongly indicates a general role of LCPAs in silica biomineralization. Graphical Abstract