During the end of the Upper Palaeolithic (11,000 BP) Franchthi Cave was no longer used. The Mesolithic era at Franchthi covers the period from 9500-8000 BP. For this period, researchers have determined two cultural phases: the Lower Mesolithic (9500-9000) and the Upper Mesolithic (9000-8000 BP).

In these phases the cave was inhabited on a permanent basis by a small community of hunters-gatherers. Their diet included red deer, wild pigs and small carnivores together with land and marine shells. One of the economic activities of the Mesolithic hunters was fishing, as the vertebrae from tuna found clearly proves, a case also known at Cyclops Cave at Yioura.

The stone industry during the Lower and Upper Mesolithic included geometric microliths and backed blades respectively. Both phases abound in denticulate implements and notches. The materials used were flint and Melian obsidian. Tracing obsidian at Franchthi, combined with fishing in the open sea, is clear evidence of early navigation in the Aegean. The presence of andesite querns (volcanic rock) imported from the islands of the Saronic Gulf indicates that those primary seamen possessed a spirit of exploration.

The querns used to grind plants and grains as well as to shape shell and stone ornaments, together with carbonized wild barley, oat and wild lentil suggest that some kind of cultivation of these plants took place. Plant gathering included among others lithospermum, almonds and pistachios.

Near the entrance of the cave there was a permanent place of internment (cemetery), where infants, children and adults - men and women- were buried (9500-9000 years BP). Among the 12 people found, it is for the first time in the Greek area that cremations were practised besides the simple inhumations. The large number of dead buried close to the habitations, also noted at Maroulas on Kythnos, confirms the permanent character of settlements during the Mesolithic Period.