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A morphological species concept distinguishes species using morphology: measurable differences in form or structure. It can be applied to preserved specimens and fossils when mating cannot be observed. Similar appearance need not imply the same species, and different appearance need not imply different species. ^[ref]

An original operational example is to compare a chosen structure in specimens of comparable age, sex and rearing conditions. Suppose two apparent groups differ in size, but one group contains only juveniles. The observed difference does not yet diagnose two species. Specify the measured phenotype, variation within each sample, and whether the distinction persists across comparable specimens. A single striking specimen is a poor substitute for that comparison.

The biological species concept groups natural populations that actually or potentially interbreed and are reproductively isolated from other such groups. Its central criterion is reproductive isolation and gene flow, rather than visible similarity. It is hard to apply directly to fossils, organisms reproducing strictly by asexual reproduction, and geographically separated populations whose potential interbreeding cannot be tested.

The phenetic species concept groups organisms by overall similarity in measured phenotypic traits. A practical morphological species concept uses anatomical form as its main evidence; strict phenetic classification can combine many kinds of measured traits. This makes such approaches usable for preserved specimens and much of the fossil record, but the decision depends on which traits are measured and how similarities are weighted.

At least four difficulties arise. Cryptic species may be reproductively isolated while looking nearly identical, so similarity can lump separate lineages. Conversely, sexual dimorphism, juvenile/adult differences and phenotypic plasticity can make one interbreeding species look like several, causing over-splitting. Convergent evolution can make distantly related organisms resemble one another in ecologically selected traits. Finally, continuous geographic or temporal variation supplies no unique gap at which to place a boundary: character choice, sample size, preservation and similarity thresholds can alter the inferred species delimitation. These are distinct from the biological concept's practical difficulty of testing actual interbreeding.

A species concept based on overall measured similarity among organisms, with explicit or implicit choices of characters, weights and grouping thresholds. A morphological species concept emphasizes anatomical similarity, while phenetic comparisons can use a wider range of phenotypic traits. Cryptic species, phenotypic plasticity, sexual dimorphism and convergent evolution explain why similarity need not coincide with reproductive isolation or a unique evolutionary lineage.

Species delimitation infers the boundaries and number of species from evidence. No single arbitrary percentage of nucleotide sequence difference is a universal boundary. Divergence within an old, widespread species can exceed divergence between recently separated species; geography and multiple kinds of evidence matter. ^[ref]

An original counterexample to a universal percentage rule: an assay could examine a strongly conserved gene in one comparison and a rapidly changing nucleotide sequence in another. Equal percentages then answer different historical questions. Even the denominator needs specifying: all sites, aligned sites, or only a filtered region? A threshold is an operational rule for a stated assay and group of organisms, whose errors need evaluating. It is not a definition that automatically transfers to every species.

The diagram's hypothetical pair B has similar morphology but reduced mating and distinct ancestry evidence. A morphological species concept could miss that distinction. Pair C instead has different morphology but compatible mating and ancestry that fails to separate the samples. That combination calls for checking variation in phenotype within a species. Pair A has only a structural difference observed: the other criteria remain untested. These examples show why missing evidence, disagreeing evidence and agreeing evidence require different interpretations.