Our work depicts a familial Duchenne muscular dystrophy case with a complex structural variant (cxSV) and a manifesting pregnant woman. Were our aims to provide molecular diagnosis and hypothesize mechanisms underlying the origin of the cxSV. We implemented a multi-technique approach including MLPA, STRs-segregation, AR-assay, SNP-array, WGS and a bioinformatic algorithm for identification of double strand breaks (DSB) stimulator motifs. We established the carrier status of the prenatal sample and explained its mother´s symptomatology by skewed X-chromosome inactivation. Furthermore, an ancestral familial ex38-43 duplication plus a de novo ex45-54 deletion was revealed in the proband, who carried the cxSV in a recombinant maternal X-chromosome. Characterization of cxSV´s breakpoints junction and its surrounding sequences allowed us to identify DSB stimulator motifs. The replication-dependent “Fork Stalling and Template Switching” mechanism was predicted to be the most likely scenario for the duplication´s origin. Whilst, the de novo deletion could arise from a germline event of inter-chromosome non-allelic recombination involving the “Non-Homologous End Joining” mechanism. The multi-technique strategy enabled precise diagnosis, accurate genetic assessment and widen the understanding of the molecular mechanisms involved in SVs’ generation. Finally, the further comprehension of the occurrence of DMD variants, favors the development of new gene therapy strategies.