The systematic and long-term use of pesticides in fruit plantations leads to the formation of resistant pest populations. The purpose of this work was to evaluate the effectiveness of the use of entomophages and acariphages for the protection of apple orchards. Against the dominant pest Cydia pomonella (Linnaeus), Habrobracon hebetor (Say) was used, which was caught in the Krasnodar Territory using cassettes with caterpillars attractive to H. hebetor. To determine the most genetically high-quality population, an RAPD analysis was carried out from three Russian (Krasnodar, Stavropol, and Belgorod) and one Kazakh (Shymkent) populations of H. hebetor, which revealed a high level of DNA polymorphism and genetic diversity in the studied geographical populations of the cities of Krasnodar and Stavropol. The efficiency of the captured Krasnodar population of H. hebetor against C. pomonella was about 75%. To regulate the number of aphids Aphis pomi De Geer and Tetraneura caerulescens (Pass.), breeding reserves of the aphidophages Harmonia axyridis Pallas, Leis dimidiata Fabr., Cycloneda sangvinea L., and Aphidius colemani Vier. were established. The biological efficiency of the developed technique was 82.8–88.6%. The release of the acariphages Amblyseius andersoni (Chant) and Metaseiulus occidentalis (Nesb.) on the apple tree showed effectiveness from 80 to 90% against Tetranychus urticae Koch and Panonychus ulmi (Koch). To study the possibility of simultaneous use of entomophages and insecticides, experiments were carried out to study the sensitivity of H. hebetor and H. axiridis to insecticides. When H. hebetor cocoons were treated with Insegar® and Atabron®, the ectoparasitoid emergence values were 98.4% and 100%, respectively. The survival of adult H. axiridis treated with Madex twin®, Atabron®, and Koragen® on the fifth day was 97.3%, 89.6%, and 81.9%, respectively. Based on the data obtained, it can be argued that it is possible to create favorable conditions for entomophages, which effectively regulate pest numbers in apple orchards.