Mitochondrial cox1 and nuclear ribosomal ITSs are commonly combined to distinguish Schistosoma species and identify hybrids in endemic countries but very rarely applied to patients diagnosed in Europe despite the increasing arrival of migrants in southwestern Europe. To assess whether those migrants are carriers of pure or hybrid schistosomes, a complete genetic characterization of Schistosoma entering Spain is performed. A total of 759 eggs (from urine + stools) from 58 patients from 8 African countries were individually processed to describe their mito-nuclear signature by cox1 rapid diagnostic multiplex one-step polymerase chain reaction (RD-PCR) and ITS-2/18S sequencing and haplotype identification by means of the complete ITS1-5.8S-ITS2 rDNA and cox1 sequencing. Combined nuclear and mitochondrial DNA markers in sub-Saharan migrants residing in Spain are described for the first time. Twenty-two (40.74%) patients were simultaneously carrying pure and hybrid eggs in their urine. Schistosoma haematobium × S. bovis (68.18%) and S. haematobium × S. curassoni (31.82%) hybrid combinations were the most frequent. Six (one pure and five hybrid) and two (pure) mito-nuclear signatures, in urine and stools, respectively, and 12 nuclear and 61 mitochondrial imported haplotypes were found. This study highlights the genetic complexity of pure and hybrid schistosomes that enter Spain, and consequently Europe, and contributes to the following: correlate the geographical origin of patients with pure and/or hybrid genetic types; detect the presence of hybrids "at distance" (hybrids in migrants from Guinea-Bissau and Mauritania are first time detected); correlate molecular haplotypes with pathologies, clinical pictures, and treatment responses; and, importantly, warn about possible sources of autochthonous transmission.