The 16S-23S rRNA Internal Transcribed Spacer (ITS) is a commonly employed taxonomic marker in cyanobacterial systematics. Due to numerous challenges in articulating phylogenetic relationships within this ubiquitous, ancient lineage, a polyphasic approach including 16S rRNA sequence data, ecology, morphology, and ITS secondary structure analysis has become the standard. In particular, the ITS motifs are being utilized in the erection of novel and cryptic taxa. However, this is challenging as researchers must manually mine and parse sequence data to visually find and identify ITS structures. This painstaking process deters researchers from using ITS motifs, may lead to inconsistencies, and is a rather dry, tedious enterprise. Thus, we present a simple, user-friendly web-based application for help in finding and preparing the most common cyanobacterial motifs (e.g., the Box-B, D1-D1´, tRNAs, etc.). After extensive testing, we note that the most common motifs are recovered at ca. 97%. These motifs can then be easily exported into Mfold or other similar folding packages. We hope that this will both provide a valuable tool for researchers but will also facilitate new discoveries and allow for greater consistency in publishing ITS comparisons. The tool can be accessed at www.phylo.dev.