Macrogyrodactylus congolensis (Prudhoe, 1957) is one of six species of Macrogyrodactylus, all of which are endemic to Africa. This monogenean is a host-specific ectoparasite of the African sharptooth catfish, Clarias gariepinus (Burchell, 1822). It attaches to the host with a posterior haptor armed with sclerites. The specific morphology of sclerites is taxonomically significant and usually studied using light microscopy. The aim of the present study was to confirm the identification of macrogyrodactylid parasites using classic morphology (light microscopy of glycerine ammonium picrate mounted specimens) and molecular techniques (18S rDNA, ITS rDNA and cytochrome oxidase subunit 1 (COI) mtDNA). Additionally, the sclerites were accurately described with a technique not previously used for the genus, whereby haptoral sclerites were isolated by removing the encapsulating soft tissue with a digestion buffer and studied with scanning electron microscopy (SEM). Morphology and morphometry of studied specimens corresponded to available data for M. congolensis, confirming the identity of the parasite. All previous descriptions were summarized in a table and discrepancies discussed. Molecular analysis also confirmed the specimens to be M. congolensis, but ITS rDNA and COI mtDNA was more reliable than 18S rDNA in this regard. The isolation of haptoral sclerites and their study using SEM was successful, resolving the morphology of all sclerites. This study provided the first reconstruction of the haptor of a Macrogyrodactylus species following SEM analysis, as well as the first mtDNA for M. congolensis. Further study of isolated haptoral sclerites of other macrogyrodactylids is required to determine the full benefits of studying their isolated sclerites.