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The paper studies interspecies physiological and genetic differences between the white-collared flycatcher and the pied flycatcher of the genus Ficedula. The fact that the flycatchers are capable of interspecies hybridization is one more reason for particular interest to these species. Using our own-developed method of taking venous blood from the eye’s sinus, we took blood samples from birds in the protected area of Homilshanski Forests, Kharkiv, Ukraine, to study their leukogram patterns. The bird feathers were also collected for genetic analysis -- to identify interspecies differences with application of the ISSR technique. It was revealed that the percentage of heterophiles in the nestlings of the pied flycatcher was lower than in the nestlings of the white-collared flycatcher. The micronucleus test did not reveal any significant difference in the interspecies groups. The spectra of amplification products obtained with the primer (AGC)6 G showed that the white-collared flycatchers had a more heterogeneous structure. The study of the leukogram, micronucleus test, and the ISSR analysis can be especially effective in the study of intra-species genetic differentiation.