The palynological organic matter (both structured and amorphous) dataset was obtained from the S05B core and from 8 surface sediment samples both collected in the Mar Piccolo, a semi-enclosed marine basin located in the Central Mediterranean. The analyses performed describe the paleoenvironmental and landscape changes during the last ~12,000 years with particular reference to the rapid Holocene climate changes (e.g., 8.2 and 4.2 ka BP event). Furthermore, the analyses conducted in surface sediments allowed us to understand the role of anthropogenic activities in the deposition of palynological organic matter.