Landraces are identified for their genetic diversity and heritage value. Geographically isolated areas are gradually recognized for their agricultural diversity and importance in conservation. One of the consequences of agricultural intensification is an increase in crop uniformity and hence a reduction in the landraces’ genetic resources. Messinia, located in Southwest Peloponnese, Greece, is characterized by a diverse terrain and smallholdings. The geomorphological character of the area and farmers’ selections have led to new landraces (local varieties) with unique traits and specific adaptations. A total of 110 villages/settlements were visited between 2013–2016, aiming to explore the existing wealth of landraces and the degree of genetic erosion. The genetic material collected and the testimonies extracted from local communities were compared to data from past expeditions, gene banks, and portal databases. Of the 427 collected samples, the majority belonged to annual vegetable or pulse species, indicating the genetic diversity of the groups, which was likely related to their culinary value. Perennial crops are priced both as commercial and staple crops, with olive trees dominating the agricultural landscape. Genetic erosion and production decline were noticed for cereals. It is concluded that socio-cultural and agricultural trends have a strong influence on the survival of landraces. Without exhausting the agricultural wealth of the region, the present study suggests that Messinia is an agrobiodiversity hotspot that includes neglected crops.