[3] The marginated tortoise was formally described by German naturalist Johann David Schoepff in 1789; its specific epithet marginata is a straightforward derivation from the Latin term for 'marginated'.

Clearly distinct according to morphology and entirely allopatric, it cannot be distinguished by mtDNA cytochrome b and nDNA ISSR sequence analysis.

[4] Lineage sorting has not occurred to a considerable degree; consequently, the more geographically isolated Sardinian population is presumably of quite recent origin.

Sequence evolution at least in mtDNA is known to proceed much more slowly in some turtles and tortoises than in others;[5] the rate of the mitochondrial 12S rRNA gene in Testudo is probably a rather low 1.0–1.6% per million years (as this fits best the paleobiogeographical situation), limiting the resolution provided by molecular systematics.

[6] An extinct subspecies described as T. m. cretensis persisted on Crete before the end of the last ice age, presumably larger than mainland tortoises.

[8] A population of small and light-colored marginated tortoises exists on the southwestern coast of the Peloponnesus, between Kalamata and south of Stoupa.

The so-called "dwarf marginated tortoise" was described as a new species Testudo weissingeri, but it is not recognizably distinct phylogenetically.

Unlike the Sardinian population, it occupies an extremely restricted range with very arid habitat, and its apomorphies seem related to this.

Both have very similar bodily characteristics—oblong carapaces, large scales on the front legs, large coverings for the head and cone-like scales on the upper thighs, undivided tail coverings, moveable stomach plates, and lack of tail spikes.

According to the 2005 DNA sequence data,[4] these species do not seem to hybridize to a notable extent in the wild, though they are obviously very close relatives, and as evidenced by morphology, some allele flow still occurs, but slowly.

The ventral shell is lighter-coloured and has pairs of triangular markings with the points facing the rear of the animal.

Early in the morning, marginated tortoises bask in the sun to raise their body temperature, and then search for food.

After feeding, the tortoises return to their shelters in the hot midday hours, leaving them again in the late afternoon.

Marginated tortoises are herbivorous, their diets consisting primarily of plants from their native Mediterranean region.

The males follow the females with great interest, encircling them, biting them on the limbs, ramming them, and trying to mount them.

During copulation, the male opens his mouth, showing his red tongue and making loud cries.

On top of this floats the embryonal disk, surrounded by albumen, so the tortoise eggs cannot be turned after the yolk settles without damaging or killing the embryo.

In nature, the animal remains below ground for the first two weeks, where it is safe from predators, yet is still able to grow, as it is nourished by the yolk sac.