Epidermolysis bullosa (EB) is a heterogeneous group of heritable blistering diseases. We developed a next generation sequencing (NGS) panel covering 21 genes associated with skin fragility disorders, and it was applied to DNA from 91 probands with the diagnosis of EB. In one patient, novel homozygous mutations were disclosed in two different, unlinked EB‐associated genes: EXPH5, chr11 g.108510085G > A; p.Arg1808Ter and COL17A1, chr10 g.104077423delT; p.Thr68LeufsTer106. Consequences of the COL17A1 mutation were examined by RNAseq which revealed a complex splicing pattern predicting synthesis of a truncated polypeptide (85%) or in‐frame deletion of exon 4 (15% of transcripts). Transmission electron microscopy (TEM) and immunostaining revealed findings consistent with EB simplex (EBS) and junctional EB (JEB), and clinical examination revealed a complex phenotype with features of both subtypes. This case illustrates the power of next generation sequencing in identifying mutations in patients with complex EB phenotype, with implications for genotype–phenotype correlations, prenatal testing, and genetic counseling of families at risk for recurrence. Epidermolysis bullosa, the paradigm of heritable skin fragility disorders, is caused by mutations in 20 distinct genes. In this study, by using whole exome sequencing and homozygosity mapping, we identified a patient with double homozygous mutations in two distinct genes (EXPH5 and COL17A1). The results emphasize the power of next generation sequencing in identifying mutations in patients with complex phenotypes, with implications for prenatal testing and genetic counseling of families at risk for recurrence.