In scientific classification, a cryptic species complex is a group of organisms that are typically very closely related yet their precise classification and relationships cannot be easily determined. Usually, when a cryptic species complex has been discovered, the individual species within the complex were separated by analysing data from multiple sources, such as by comparing polytene chromosomes, DNA sequence analyses, bioacoustics and thorough life history studies. The members of a cryptic species might or might not constitute a superspecies, in other words they might appear very similar but not be very closely related.
The component species of a cryptic species complex may be parapatric, are frequently sympatric, and are sometimes allopatric. Cryptic species complexes are not the same as populations undergoing speciation: they typically represent a situation where speciation has already broken the gene flow between populations, but where evolution has not progressed to a point where easily recognizable adaptations have taken place.
Cryptic species may be somewhat more distantly related and simply represent lineages that have been so successful as to require little evolutionary change, possibly coupled with parallel evolution. A famous example are the Eurasian Treecreeper and Short-toed Treecreeper. These birds were perhaps the first cryptic species to be recognized as such (by Christian Ludwig Brehm in 1820). Other ornithologists refused to accept that more than one species was involved until Brehm presented his bioacoustic studies, which left no room for doubt. The European Treecreeper has since been found to be a very close relative of the Himalayan Hodgson's Treecreeper, while the Short-toed Treecreeper is probably the sister species of the North American Brown Creeper. Cryptic species are also common in certain families of insects such as Chironomidae.
It has been suggested that cryptic species complexes are very common in the marine environment. Although this suggestion antedated the detailed analysis of many systems using DNA sequence data, it has been proven correct. The increased use of DNA sequence in the investigation of organismal diversity (also called Phylogeography and DNA barcoding) has led to the discovery of a great many cryptic species complexes in all habitats. In the marine bryozoan Celleporella hyalina, detailed morphological analyses and mating compatibility tests between the isolates identified by DNA sequence analysis were used to confirm that these groups consisted of more than 10 ecologically distinct species that had been diverging for many million years.
Evidence from the identification of cryptic species has led some[who?] to conclude that current estimates of global species richness are too low. For example, mitochondrial DNA research published in January 2008 suggests that there are at least 11 genetically distinct populations of giraffes. Similar methods also found that the Amazonian frog Eleutherodactylus ockendeni is actually at least 3 different species that diverged over 5 million years ago.