The West Indian top shell (Cittarium pica) is a key fishery resource in many Caribbean areas. This mollusk lives in intertidal and shallow subtidal conditions on rocky shores and has a short-lived larval phase (<5 days). On the other hand, it is overexploited in a large part of its distribution and listed in the red books of threatened species. Despite its well-recognized conservation importance, there is a lack of molecular resources currently available. For this reason, we used the double digest restriction site- associated DNA sequencing (ddRad-seq) to evaluate the population genomic structure across the Colombian Caribbean. 65 samples were collected in five locations (Cabo de la Vela=12; Santa Marta=15; Cartagena=8; Isla Fuerte=15; Capurganá=15) between 2017 and 2018. A total of 55,112 SNPs were identified, with 35,594 of them being on average polymorphic. Several analyses about the genetic structure performed with AMOVA (Fst=0.224; p<0.05), PCoA, Structure (K=3), and an ML tree (3 clusters) indicated that C. pica presents three populations (pop 1: Cabo de la Vela; pop 2: Santa Marta; pop 3: Cartagena+Isla Fuerte+Capurganá). Interestingly, all the analyses showed a genetic break between Cabo de la Vela and Santa Marta (Fst=0.175; p<0.05) due to the absence of rocky shore habitats along the 300 km of coastline. We discuss that C. pica is a good biological model to explain how the southern Caribbean biogeographic barrier operates for those marine organisms that live on rocky intertidal habitats and exhibit a short-lived larval phase or lack it completely. Consequently, these findings open a new debate about the importance of evaluating the effects of the barrier on other aspects of these marine organisms. Finally, the results will improve the management and conservation strategies proposed for C. pica in Colombia.