Fraser syndrome (FS) is a phenotypically variable, autosomal recessive disorder characterized by cryptophthalmus, cutaneous syndactyly and other malformations resulting from mutations in FRAS1, FREM2 and GRIP1. Transient embryonic epidermal blistering causes the characteristic defects of the disorder. Fras1, Frem1 and Frem2 form the extracellular Fraser complex, which is believed to stabilize the basement membrane (BM). However, several cases of FS could not be attributed to mutations in FRAS1, FREM2 or GRIP1, while Fraser syndrome displays high clinical variability, suggesting there is an additional genetic, possibly modifying contribution to this disorder. AMACO, encoded by the VWA2 gene, has a very similar tissue distribution to the Fraser complex proteins in both mouse and zebrafish. Here, we show that AMACO deposition is lost in Fras1 deficient zebrafish and mice and that Fras1 and AMACO interact directly via their CSPG and P2 domains. Knockdown of vwa2, which alone causes no phenotype, enhances the phenotype of hypomorphic Fras1 mutant zebrafish. Together, our data suggest that AMACO represents a novel member of the Fraser complex.