Sea urchins (echinoids) are common model organisms for research in developmental biology and for their transition from a bilateral larva into their post-metamorphic adult with pentaradial body symmetry. The adult also has a calcareous endoskeleton with a multimetameric pattern of continuously added elements, among them the namesake of this phylum, spines. Nearly all echinoids have both large primary spines, and an associated set of smaller secondary spines.We hypothesize that the secondary spines of the tropical variegated urchin species, Lytechinus variegatus, are morphologically and molecularly distinct structures from primary spines and not just small spines. To test this premise, we examined both spine types using light microscopy, micro-CT imaging, lectin labeling, transcriptomics, and fluorescent in situ hybridization (FISH). Our findings reveal basic similarities between the two types in mineral and cellular anatomy, but with clear differences in growth patterns, genes expressed, and in the location of gene expression within the two types of spines. In particular, secondary spines have non-overlapping, longitudinally concentrated growth bands that lead to a blunt and straight profile, and a distinct transcriptome involving the upregulation in many genes in comparison to the primary spines. Neural, ciliary, and extracellular matrix interacting factors are implicated in the differentially expressed gene (DEG) dataset, including two genes - ONECUT2 and an uncharacterized discoidin- and thrombospondin-containing protein - that show spine type- specific localizations in FISH, and may be of interest to ongoing work in urchin spine patterning.These results demonstrate that primary and secondary spines have overlapping but distinct molecular and biomineralized characteristics, suggesting unique developmental and regenerative mechanisms, and devotion to this spiny dermal phylum. Overall design: For transcriptomic analysis, 50 primary and 100 secondary spines each were harvested from 4 wild-caught L. variegatus individuals. All individuals chosen were of the white-and-green color morph, in order to avoid potential confounds due to genetic and transcriptomic differences between morphs (for discussion of color morph effects in this species, see (Moscoso, 2015 Pawson and Miller, 1982 Wessel et al., 2024) . Spines were immersed in TriZol and RNA was extracted following the manufacturer’s instructions. The resulting 4 primary and 4 secondary samples were sent to NovoGene for comparative RNAseq analysis, with the echinobase.org L. variegatus assembly v3.0 as the reference genome.