Clathrina aurea was considered endemic to Brazil before being recorded from the Pacific (Peru) and the Caribbean Sea. We assessed the morphological variability, phylogeographic pattern and population genetic structure of the species across its geographic range to understand how habitat fragmentation/reduction can affect a widely distributed species with supposedly low dispersal capability. Samples from 15 localities in the Caribbean Sea (n = 8), Brazil (n = 5), and Peru (n = 2) were studied. Morphological analyses included characterisation of external morphology, skeleton composition, and spicules morphometry. Phylogenetic trees and haplotype network were constructed using rDNA sequences. Population structure was assessed using microsatellite loci (FST fixation index and Discriminant Analysis of Principal Components). Morphological traits were consistent with C. aurea, although certain differences have been found, possibly due to environmental factors (temperature and pH). Phylogenetic analyses corroborated the conspecificity of the individuals and indicated higher genetic variability in individuals from Brazil and Caribbean, compared to Peru. Phylogeographic analyses indicated that Brazil had the oldest population of C. aurea, suggesting the expansion of this species across the Amazon River to the Caribbean and its connectivity through intermediate populations (e.g., Abrolhos). Population structure analyses also revealed high levels of genetic connectivity between the Caribbean and Northeast Brazil and among Southeast Brazilian localities. All analyses indicated isolation or restricted gene flow between Pacific and Atlantic populations. This, combined with the reduced genetic diversity in Peru and the supposedly limited larval dispersal capability, suggest a possible non-natural dispersion; however, we cannot exclude other hypotheses.