Apple (Malus domestica Borkh.) rootstocks play a key role in modern intensive orchard systems, where their accurate identification is essential for breeding, nursery production, and certification of planting material. This is particularly important in Kazakhstan, a recognized center of origin of cultivated apple, where local germplasm remains insufficiently characterized at the molecular level. In this study, we integrated simple sequence repeat (SSR) genotyping and morphological trait analysis to develop a reliable approach for the identification of clonal apple rootstocks cultivated in Kazakhstan. Five widely used rootstocks (Zhetysu 5, ARM-18, B-7-35, M9, and B9) were analyzed using 17 polymorphic SSR markers and 30 vegetative traits. SSR analysis revealed moderate genetic polymorphism (PIC = 0.28–0.54; He = 0.35–0.58) and enabled clear discrimination among all studied genotypes. Cluster analysis based on genetic distances grouped rootstocks according to their genetic similarity, reflecting their origin and differentiation. Morphological evaluation demonstrated significant phenotypic variability and identified correlations among key vegetative traits related to plant vigor and leaf development. The integration of molecular and morphological data allowed the development of comprehensive genotype profiles (“molecular–morphological passports”) for each rootstock, ensuring their reliable identification. The proposed approach provides a practical framework for the certification of planting material and the management of apple genetic resources in Kazakhstan. It can be applied to improve nursery systems, support breeding programs, and ensure the production of true-to-type planting material in modern horticulture.

Latent viral and viroid infections represent a major phytosanitary threat to pome fruit production because infected propagation material facilitates the long-term spread of pathogens in orchards. This study investigated the prevalence of viral and viroid pathogens in apple and pear orchards of southern and southeastern Kazakhstan and evaluated the efficiency of integrated in vitro sanitation approaches. A total of 34 samples collected from commercial orchards were analyzed using RT-qPCR. Apple stem pitting virus (ASPV) was the most prevalent pathogen detected across all surveyed regions, followed by Apple chlorotic leaf spot virus (ACLSV). Apple stem grooving virus (ASGV), Apple hammerhead viroid (AHVd), Apple mosaic virus (ApMV), and Apple rubbery wood virus 1 (ARWV-1) were detected at lower frequencies. Notably, ARWV-1 and AHVd were detected exclusively in the Almaty Region, representing their first molecular detection in Kazakhstan. Mixed infections were common, and visual symptoms did not consistently correlate with molecular detection results, emphasizing the importance of RT-qPCR for reliable phytosanitary diagnostics. Integrated sanitation methods combining thermotherapy, chemotherapy, cryotherapy, and meristem culture effectively eliminated viral and viroid infections from infected apple and pear genotypes. Ribavirin at 15 mg L⁻¹ provided the optimal balance between antiviral activity and explant viability. Complete elimination of ACLSV, AHVd, ASPV, ASGV, ApMV, and ARWV-1 was achieved after combined treatment, while regenerated plants maintained stable micropropagation capacity. The obtained results demonstrate the necessity of routine molecular monitoring and support the development of virus-free certification systems for pome fruit crops in Kazakhstan.