BackgroundAmong both plants and arthropods, super-hydrophobic surfaces have evolved that enable self-cleaning, locomotion on water surfaces, or plastron respiration. Super-hydrophobicity is achieved by a combination of non-polar substances and complex micro- and nano-structures, usually acquired by growing processes or the deposition of powder-like materials.ResultsHere we report on a multi-phasic secretion in whip spiders (Arachnida, Amblypygi), which externally forms durable, hierarchical microstructures on the basically smooth cuticle. The solidified secretion crust makes the previously highly wettable cuticle super-hydrophobic. We describe the ultrastructure of secretory cells, and the maturation and secretion of the different products involved.ConclusionWhip spiders represent intriguing objects of study for revealing the mechanisms of the formation of complex microstructures in non-living systems. Understanding the physical and chemical processes involved may, further, be of interest for bio-inspired design of functional surface coatings.Electronic supplementary materialThe online version of this article (doi:10.1186/s40851-016-0059-y) contains supplementary material, which is available to authorized users.