Economic theory predicts positive effects of market liberalisation on market efficiency and integration. This paper investigates the effects of liberalisation on dry beans markets systems in Malawi. It also investigates the nature of structural relationships existing within each market system. The analysis relies on structural vector equilibrium correction models (SVECM). The results suggest that dry beans markets in Malawi are integrated and markets within the Southern region market system share stronger links in the short-run than those in other regions of Malawi. The analysis also reveals that peripheral markets drive prices in central markets.