The species problem is a mixture of difficult, related questions that often come up when biologists define the word "species". Definitions are usually based on how individual organisms reproduce, but biological reality means that a definition that works well for some organisms (e.g., birds) will be useless for others (e.g., bacteria).
One common, but sometimes difficult, question is how best to decide which species an organism belongs to, because reproductively isolated groups may not be readily recognizable; cryptic species may be present.
Another common problem is how to define reproductive isolation, because some separately evolving groups may continue to interbreed to some extent, and it can be a difficult matter to discover whether this hybridization affects the long-term genetic make-up of the groups.
Many of the debates on species touch on philosophical issues, such as nominalism and realism, as well as on issues of language and cognition.
The current meaning of the phrase "species problem" is quite different from what Charles Darwin and others meant by it during the 19th and early 20th centuries. For Darwin, the species problem was the question of how new species arose: speciation.
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“Thus all probable reasoning is nothing but a species of sensation. ‘Tis not solely in poetry and music, we must follow our taste and sentiment, but likewise in philosophy, When I am convinc’d of any principle, ‘tis only an idea which strikes more strongly upon me. When I give the preference to one set of arguments above another, I do nothing but decide from my feeling concerning the superiority of their influence.”
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