Hydatidosis is caused by a tapeworm which infects humans by the larval stage. In humans, the disease is so serious that it requires surgery for treatment. Documents show that there have been many efforts in finding new scolicidal agents for reducing the rate of the infection. The objective of this study was determination of the scolicidal effect of two fungal chitosan types, produced from Penicillium spp. and commercially chitosan (CC) on Echinococcus granulosus protoscolex. Protoscolices were aseptically aspirated from sheep livers hydatid cysts. Four concentrations (50, 100, 200, 400 μg/ml) of each type of prepared chitosan were used for 10, 30, 60 and 180 min. Viability of protoscolices was detected by 0.1 % eosin staining. Fungal chitosan which was the most bioactive type with higher degree of deacetylation showed stronger scolicidal activity in vitro (P < 0.05). Fungal chitosan could be recommended, as good as CC for hydatid cysts control and is a noble alternative for synthetic and chemical scolicidal.