Freshwater organisms with an amphidromous life cycle are generally thought to disperse widely through marine planktonic larval stages, but only few studies on genetic population structure of amphidromous shrimp exist. We used a 640-basepair region of the mitochondrial gene cytochrome c oxidase I (Cox1) from the amphidromous river shrimp Cryphiops caementarius from five rivers in northern-central Chile to test whether large distances between estuaries (up to 700 km) limit gene flow between populations and result in genetic differentiation among populations. The results revealed high haplotype diversity with no significant geographical structuring, suggesting that gene flow occurs regularly over several hundreds of kilometres, also connecting populations north and south of the Atacama Desert. Seemingly, the terrestrial barrier is overcome by planktonic larval dispersal through the sea, suggesting wide dispersal rather than “stepping-stone” dispersal between estuaries. The population from the southern limit of the geographic distribution of C. caementarius (Río Limari) revealed some weak differentiation in pairwise Φ_ST comparisons, but larger sample sizes are necessary to confirm this. Additional studies are needed for a better understanding of factors that promote different life histories, like marine planktonic dispersal, larval retention in estuaries, or an amphidromous-freshwater transition towards a purely freshwater life cycle.