During the Neolithic period, near the North-Eastern coast of the Gargano promontory (Apulia Region, Italy), an important network of mines represented the most ancient European example of systematic exploitation of primary chert sources. These high-quality raw materials were traded between prehistoric communities living on both sides of the Adriatic Sea. However, the Gargano promontory is not the only area of the Apulia Region with chert sources. Secondary sources of the Tavoliere plain deposits and primary sources of the Southern Apennines must be considered in addition to the Gargano chert-bearing limestones. This paper provides an overview of chert sources distribution in the Gargano and Tavoliere plain through a chert sources map based on up-to-date geological and archaeological information. The map represents the first lithic procurement mapping in the Region and it is a very useful tool for planning sampling activities and detect the potential chert sources exploited in Neolithic times. The map was used for sampling pebbles near the coast and inland of the investigated area. A non-destructive multi-parametric protocol for chert investigations (NM-PCI) method was applied to all the collected secondary samples. The results were compared at first with those of the Gargano mines. The output of the partition around medoids (PAM) procedure shows, as a general trend, that primary sources are well grouped, while secondary sources show less clear compositional fingerprints. However, the features of the coastal and inland pebbles are quite different.