Most of the cysteine proteases (CPs) expressed by ectoparasites belong to the papain-like superfamily (clan CA, family C1) and are associated with the physiological events during different developmental life stages. Cathepsins, legumains/asparaginyl endopeptidases and caspases (clan CA, family C1, C13 and C14, respectively) play a major role in mosquito biology. There is accumulating evidence that CPs expressed by arthropods may play a role in clinical presentations of some transmitted parasitic disease, e.g. babesiosis. During blood meals, salivary glands secrete bioactive substances, including CPs, to exert several pharmacological properties that assist ectoparasites to evade host defense responses and to induce inflammatory reactions. Furthermore, they play an important role in extracellular and intracellular proteins degradation as well as their processing. In this regard, cystatins (CYSs) were found to inhibit insect CPs suggesting its use as targets for control of mites and ticks. The present review aims to identify different CPs expressed in ectoparasites, the main vectors of several endemic diseases such as malaria, babesiosis, Chagas' and Lyme disease. Meanwhile, it highlights different CYSs that could be used as biological insecticides to control diseases transmitted by mites and ticks.