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The freshwater snail genus <i>Bulinus</i> plays a vital role in transmitting parasites of the <i>Schistosoma haematobium</i> group. A hybrid schistosome between <i>S. haematobium</i> and <i>S. mattheei</i> has been recently detected using DNA-based identification methods in school children along the Lake Malawi shoreline in Mangochi District. This finding raised the need for contemporary revaluation of local interactions between schistosomes and snails, with a particular focus on snail species within the <i>Bulinus africanus</i> group. In 2017 and 2018, malacological surveys sampled several freshwater sites in Mangochi District. Collected snails (<i>n</i> = 250) were characterised using cytochrome oxidase subunit 1 gene (<i>cox</i>1), with DNA barcoding of the ‘Folmer’ region and a rapid PCR-RFLP typing assay with double digestion with <i>Hae</i>III and <i>Sac</i>I restriction enzymes. DNA <i>cox</i>1 sequence analysis, with phylogenetic tree construction, suggested the presence of at least three <i>B. africanus</i> group taxa in Lake Malawi, <i>B. globosus,</i> alongside first reports of <i>B. africanus</i> and <i>B. angolensis,</i> which can be differentiated by PCR-RFLP methods. In addition, a total of 30 of the 106 <i>B. africanus</i> group snails (28.30%) were positive to the <i>Schistosoma</i>-specific screen using real-time PCR methods. This study provides new insight into the recent changes in the epidemiology of urogenital schistosomiasis as likely driven by a new diversity of <i>B. africanus</i> group snails within the Lake.