We investigated how large populations of several mysid species can coexist in oligotrophic underwater marine caves and their relationships in the marine cave food web using carbon and nitrogen stable isotopes. Isotopic signatures indicate food partitioning among the 5 species of cave-dwelling mysids from the northwest Mediterranean Sea we studied. Hemimysis speluncola feeds mainly on phytoplankton and zooplankton from outside the caves, Siriella gracilipes on sedimentary organic matter and zooplankton from outside, Harmelinella mariannae on small cave-dwelling crustaceans, and Hemimysis margalefi and Hemimysis lamornae mediterranea on sedimentary particulate organic matter. These differences in diet could promote coexistence of such diverse and abundant mysid faunas in marine caves by reducing interspecific competition for scarce resources. The analysis of both seston and cave sediments revealed that the quantity and quality of organic matter are strongly reduced in marine caves, suggesting that cavedwelling mysids find most of their food elsewhere. This inference agrees with documented distributions of some of these mysids outside of caves at night where they can feed in the rich littoral zone. These migrations of some species make cave-dwelling mysids important vectors of organic matter transfer from the outside euphotic littoral zone to various locations inside caves. Outside organic matter is then made available to other cave dwellers through mysid fecal pellet production and predation, as suggested by the isotopic compositions of predators like teleost fishes, decapod crustaceans, and carnivorous cladorhizid sponges.

The marine cave‐dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea, which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographical regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean Sea through the use of several mitochondrial and nuclear markers. Five deeply divergent lineages were observed among H. margalefi populations resulting from deep phylogeographical breaks, some dating back to the Oligo‐Miocene. Whether looking at the intralineage or interlineage levels, H. margalefi populations present a high genetic diversity and population structuring. This study suggests that the five distinct lineages observed in H. margalefi actually correspond to as many separate cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds to the westernmost lineage here surveyed from the Alboran Sea to southeastern Italy. Typical genetic breaks such as the Almeria‐Oran Front or the Siculo‐Tunisian Strait do not appear to be influential on the studied loci in H. margalefi sensu stricto. Instead, population structuring appears more complex and subtle than usually found for model species with a pelagic dispersal phase. The remaining four cryptic taxa are all found in the eastern basin, but incomplete lineage sorting is suspected and speciation might still be in process. Present‐day population structure of the different H. margalefi cryptic species appears to result from past vicariance events started in the Oligo‐Miocene and maintained by present‐day coastal topography, water circulation and habitat fragmentation.