Research on abiotic stress tolerant horticultural plants has been widely carried out. However, there has not been much research on the citrus phenotype with rootstock as planting material, which has advantages in overcoming abiotic stress and dwarf performance. This research provides citrus rootstock that is tolerant to some of the marginal land in Indonesia especially on drought, salinity, waterlogging, and acidity. This morphological research was conducted at Punten Experimental Garden in Batu city, Indonesia. Anatomical observations were carried out in the laboratories of Indonesian Balitjestro and Universitas Brawijaya. This has done pre-treatment selection lasted for 8 months and then abiotic stress treatment lasted for 2 months, from July to September 2021. This study consisted of 15 treatment combinations: three rootstock varieties, i.e., Citromello (Cit), Volkameriana (Volk), and Cleopatra mandarin (CM), and five abiotic stress treatments, i.e., control, PEG 10%, NaCl 3.5%, waterlogging 150% FC, and 9 mM Al2SO4. The results showed that abiotic stress, especially NaCl and waterlogging, caused phenotypic changes such as in leaf shape, i.e., leaf lamina shape, reduced leaf area, chlorophyll content, stomata density, and canopy diameter compared to other abiotic stresses. The best stomatal density and open stomata percentage were for Cleopatra mandarin (CM). This was also shown by the increase in proline content when plants are subjected to abiotic stresses, especially in Cleopatra mandarin under NaCl stress, Volkameriana under Al2SO4 stress, and Citromello under waterlogging (WL). The palisade size decreased, its vascular bundles in the leaves increased, and the pore distribution changed. The results showed all rootstock candidates were resistant to several abiotic stresses and had dwarf performance. It can be concluded that the best tolerant of abiotic stress rootstock variety of abiotic stress is Cleopatra mandarin, while Volkameriana and Citromello are better tolerant on acidic soil.