Efficient DNA extraction is a keystone in molecular assays. A wide range of methods is used to extract DNA from biological materials. These methods vary in their efficiency, economic costs, and availability. Therefore, the present study was conducted to assess the efficiency of a Hotshot method for DNA extraction from minute fish trematodes in comparison to a commercial kit. A total of 68 samples were examined. Samples included 29 encysted metacercariae from the African catfish(Clarias gariepinus) collected from the Nile tributaries in Ismailia Governorate, and 39 adult trematodes collected from rats after being experimentally infected with encysted metacercariae from fish samples.  Helminths were morphologically identified where they belonged to family Cyathocotylidae, species Mesostephanus burmanicus, Prohemistomum vivax, and Mesostephanus appendiculatus. The DNA yield by the Hotshot method was compared to the commercial kit. The hotshot method produced 28% higher DNA yield per sample (mean ± SE: 2.65 ± 0.83 µg) than the commercial kit (2.07 ± 0.16 µg), but the difference was not significant (Mann-Whitney U test, P>0.05). PCR amplification success of the internal transcribed spacer 2 (ITS-2) was also higher for trematode samples extracted by the Hotshot method than the commercial kit. Although the differences were not statistically significant, the Hotshot method is still rapid, cheap, and does not require special reagents or equipment for DNA extraction from minute helminths.