Paleontology in the 21st century is a field with high interdisciplinary cooperation. Aside from the traditional morphology analysis, modern paleontologists and taxonomists can also leverage novel technical breakthroughs in molecular biology to peek into the evolutionary past. Irregular echinoids, which comprise the extant members of heart urchins (Atelostomata), sand dollars (Scutelloida), and sea biscuits (Clypeasteroida), is a subgroup of echinoids exhibiting a secondary bilateral symmetry body plan. This clade's evolution history and development remain a realm of intensive investigation that benefits profoundly from the progress of Next Generation Sequencing (NGS) technology. In this study, we reviewed the methodology and theoretical basis of molecular evolution and conducted a case study on the Taiwanese endemic sand dollar species Sinaechinocyamus mai. We exemplified the value of sequence analysis in phylogeny study and the prospect of incorporating molecular data in future investigations to shed light on the enigmatic phylogenetic relationship and body plan establishment of Scutelloida and Clypeasteroida.