An oceanographic cruise from the southern Adriatic to the northern Ionian Sea in May 2013 allowed us to describe the spatial abundance and distribution of decapod crustacean larval assemblages with a multidisciplinary approach. Seventeen locations on the Apulian and Albanian shelves and offshore waters, including the Strait of Otranto, were sampled by a BIONESS electronic multinet. A swarm of zoeae (11 Brachyura taxa, mostly at first instar, with Xantho granulicarpus at 87%) was recorded in the neuston of the Italian side. Decapod larvae were concentrated in the first 20–30 m surface layer, strongly linked to the thermocline and generally above the Deep Chlorophyll Maximum (DCM), suggesting that they are carried by surface water circulation. The migratory behavior of decapod larvae in coastal stations is quite regular at between 20 and 60 m depths and independent of the time of day. In offshore stations, migration is compatible with the day–night cycle, where a minimum Weighted Mean Depth (WMD) value is evident at about 20 m at night. The availability of four satellite-tracked surface drifters in the same area and during the period of larvae presence presented a possibility to explore the link between the geographic dispersal of larvae and their surface circulation in successive days. Only one drifter crossed the south Adriatic, passing from the Italian to the Balkan neritic area, taking about 40 days. The actual genetic homogeneity of many Brachyura coastal species populations on opposite sides of the Adriatic Sea suggests the existence of a genetic connection that does not rely exclusively on larvae circulation and appears to be fueled by additional strategies of biological communication.