Over the last 40 years, hypogenic karst/caves have become well known and hypogene speleogenesis has been used to explain the formation of some of the largest subterranean maze caves. These hypogenic systems involve confined aquifers with upwards flow, responsible for their karstification. Such spaces begun and could be remain isolated from the surface and the contiguous subterranean habitats, including the shallow ones. We studied the invertebrate fauna and the geology/speleogenesis of two recently opened caves from Eastern Iberian Peninsula, which clearly showed features of hypogenic origin. Their scarce faunistic composition, formed by non cave-adapted fauna, is similar to other hypogenic caves from Europe and North America, suggesting that there are restrictions for faunal colonization of the hypogenic subterranean ecosystems. We propose differentiating the hypogenic from the epigenic subterranean ecosystem based on the fact that the first one lacks fauna during its genesis. This new scenario may have consequences in the regional biodiversity patterns of troglobiont species.