No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species. Generally the term includes the unknown element of a distinct act of creation.
When scientists do not know whether two morphologically similar groups of organisms are capable of interbreeding; this is the case with all extinct life-forms in palaeontology, as breeding experiments are not possible.
Species identification is made difficult by discordance between molecular and morphological investigations; these can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages). In addition, horizontal gene transfer (HGT) makes it difficult to define a species. All species definitions assume that an organism acquires its genes from one or two parents very like the "daughter" organism, but that is not what happens in HGT. There is strong evidence of HGT between very dissimilar groups of prokaryotes, and at least occasionally between dissimilar groups of eukaryotes, including some crustaceans and echinoderms.
there is no easy way to tell whether related geographic or temporal forms belong to the same or different species. Species gaps can be verified only locally and at a point of time. One is forced to admit that Darwin's insight is correct: any local reality or integrity of species is greatly reduced over large geographic ranges and time periods.
Natural hybridisation presents a challenge to the concept of a reproductively isolated species, as fertile hybrids permit gene flow between two populations. For example, the carrion crowCorvus corone and the hooded crowCorvus cornix appear and are classified as separate species, yet they hybridise freely where their geographical ranges overlap.
Hybridisation of carrion and hooded crows permits gene flow between 'species'
A ring species is a connected series of neighbouring populations, each of which can sexually interbreed with adjacent related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" population. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region thus closing the ring. Ring species thus present a difficulty for any species concept that relies on reproductive isolation. However, ring species are at best rare. Proposed examples include the herring gull-lesser black-backed gull complex around the North pole, the Ensatina eschscholtzii group of 19 populations of salamanders in America, and the greenish warbler in Asia, but many so-called ring species have turned out to be the result of misclassification leading to questions on whether there really are any ring species.
Seven "species" of Larus gulls interbreed in a ring around the Arctic.