Myotis alcathoe is the smallest European Myotis species.
The fur is brownish on the upperparts, with a reddish tone in old specimens, and a slightly paler gray-brown below.
Younger animals may be completely gray-brown.
The brown fur distinguishes adult M. alcathoe from other whiskered bats, but juveniles cannot be unambiguously identified on the basis of morphology.
M. alcathoe is similar to Daubenton's bat (Myotis daubentonii) and M. emarginatus in color.
On the upper side of the body, the hairs are 6 to 8 mm long and have dark bases and brown tips.
The hairs on the lower side of the body are only slightly paler at the tip than at the base.

The face and the upper lips are reddish to pink, not dark brown to black as in M. mystacinus.
Although most of the face is hairy, the area around the eyes is bare.
The nostrils are heart-shaped, and their back end is broad, as in M. brandtii, not narrow as in M. mystacinus.
Several glands are present on the muzzle, most prominently in reproductively active males.
The ears are brown and are lighter on the inside than the outside.
There is a notch at the edge of the ear, and the pointed tragus (a projection inside the ear that is present in some bats) extends up to this notch; the tragus is longer, extending beyond the notch, in both M. brandtii and M. mystacinus.
The base of the inner side of the ear is white; it is much darker in M. mystacinus.
The feet and the thumbs are very small.
The small size of the ear, tragus, feet, and thumb distinguishes M. alcathoe from the slightly larger M. mystacinus and M. brandtii, but the feet are relatively larger than in M. mystacinus.

The wings are brown, but lighter than those of M. mystacinus.
The plagiopatagium (the portion of the wing between the last digit and the hindlegs) is attached to the fifth toe.
The tail extends only about 1 mm beyond the back margin of the uropatagium (the portion of the wing membrane between the hindlegs).
The calcar, a cartilaginous spur supporting the uropatagium, is slender.
With a width around 1.3 mm, the penis is narrow, and it lacks a broadened tip (except in one Croatian specimen).
The baculum (penis bone) is about 0.5 mm long.
The short and broad shape of this bone distinguishes M. alcathoe from M. brandtii as well as M. ikonnikovi.

The skull is similar in shape to that of M. mystacinus and M. brandtii, but the front part of the braincase is higher.
The second and third upper premolars (P2 and P3) are tiny and pressed against the upper canine (C1) and fourth premolar (P4).
The canine is less well-developed than in M. mystacinus.
There is a clear cusp present on the side of the P4.
The accessory cusp known as the protoconule is present on each of the upper molars when they are unworn.
M. mystacinus lacks the P4 cusp and the protoconules on the molars, but M. brandtii has an even larger cusp on P4.

As usual in Myotis species, M. alcathoe has a karyotype consisting of 44 chromosomes, with the fundamental number of chromosomal arms equal to 52.
However, a 1987 study already found that M. alcathoe (then called "Myotis sp.
B") differs from both M. mystacinus and M. brandtii in the pattern of active nucleolus organizer regions on the chromosomes.
M. alcathoe also differs from other Myotis species in the sequences of the mitochondrial genes 12S rRNA and NADH dehydrogenase subunit 1 by at least 5% and 13%, respectively.

M. alcathoe has the highest-frequency echolocation call of any European Myotis.
In open terrain, the call has an average duration of 2.5 ms, but it may be up to 4 ms long.
At the beginning, its frequency is around 120 kHz, but it then falls fast, subsequently falls slightly slower, and at the end falls faster again.
The call reaches its highest amplitude at around 53 kHz.
It terminates at around 43 to 46 kHz; this characteristic is especially distinctive.
In different experiments, the time between calls was found to be around 85 and 66 ms, respectively.
The high-pitched call may be an adaptation to the animal's occurrence in dense vegetation.

Head and body length is about 4 cm (1.6 in) and wingspan is
Myotis alcathoe is the smallest European Myotis species. The fur is brownish on the upperparts, with a reddish tone in old specimens, and a slightly paler gray-brown below. Younger animals may be completely gray-brown. The brown fur distinguishes adult M. alcathoe from other whiskered bats, but juveniles cannot be unambiguously identified on the basis of morphology. M. alcathoe is similar to Daubenton's bat (Myotis daubentonii) and M. emarginatus in color. On the upper side of the body, the hairs are 6 to 8 mm long and have dark bases and brown tips. The hairs on the lower side of the body are only slightly paler at the tip than at the base.
The face and the upper lips are reddish to pink, not dark brown to black as in M. mystacinus. Although most of the face is hairy, the area around the eyes is bare. The nostrils are heart-shaped, and their back end is broad, as in M. brandtii, not narrow as in M. mystacinus. Several glands are present on the muzzle, most prominently in reproductively active males. The ears are brown and are lighter on the inside than the outside. There is a notch at the edge of the ear, and the pointed tragus (a projection inside the ear that is present in some bats) extends up to this notch; the tragus is longer, extending beyond the notch, in both M. brandtii and M. mystacinus. The base of the inner side of the ear is white; it is much darker in M. mystacinus. The feet and the thumbs are very small. The small size of the ear, tragus, feet, and thumb distinguishes M. alcathoe from the slightly larger M. mystacinus and M. brandtii, but the feet are relatively larger than in M. mystacinus.
The wings are brown, but lighter than those of M. mystacinus. The plagiopatagium (the portion of the wing between the last digit and the hindlegs) is attached to the fifth toe. The tail extends only about 1 mm beyond the back margin of the uropatagium (the portion of the wing membrane between the hindlegs). The calcar, a cartilaginous spur supporting the uropatagium, is slender. With a width around 1.3 mm, the penis is narrow, and it lacks a broadened tip (except in one Croatian specimen). The baculum (penis bone) is about 0.5 mm long. The short and broad shape of this bone distinguishes M. alcathoe from M. brandtii as well as M. ikonnikovi.
The skull is similar in shape to that of M. mystacinus and M. brandtii, but the front part of the braincase is higher. The second and third upper premolars (P2 and P3) are tiny and pressed against the upper canine (C1) and fourth premolar (P4). The canine is less well-developed than in M. mystacinus. There is a clear cusp present on the side of the P4. The accessory cusp known as the protoconule is present on each of the upper molars when they are unworn. M. mystacinus lacks the P4 cusp and the protoconules on the molars, but M. brandtii has an even larger cusp on P4.
As usual in Myotis species, M. alcathoe has a karyotype consisting of 44 chromosomes, with the fundamental number of chromosomal arms equal to 52. However, a 1987 study already found that M. alcathoe (then called "Myotis sp. B") differs from both M. mystacinus and M. brandtii in the pattern of active nucleolus organizer regions on the chromosomes. M. alcathoe also differs from other Myotis species in the sequences of the mitochondrial genes 12S rRNA and NADH dehydrogenase subunit 1 by at least 5% and 13%, respectively.
M. alcathoe has the highest-frequency echolocation call of any European Myotis. In open terrain, the call has an average duration of 2.5 ms, but it may be up to 4 ms long. At the beginning, its frequency is around 120 kHz, but it then falls fast, subsequently falls slightly slower, and at the end falls faster again. The call reaches its highest amplitude at around 53 kHz. It terminates at around 43 to 46 kHz; this characteristic is especially distinctive. In different experiments, the time between calls was found to be around 85 and 66 ms, respectively. The high-pitched call may be an adaptation to the animal's occurrence in dense vegetation.
Head and body length is about 4 cm (1.6 in) and wingspan is
Alcathoe bat