Salinity is one of the most destructive environmental challenges for citriculture worldwide, and all climate change scenarios are predicting an increased impact of salinity on citrus orchards. Citrus cultivars are grown as grafts on various rootstocks to provide specific adaptation to abiotic stress and tolerance to major diseases such as citrus tristeza virus. To understand rootstock–scion interactions with regard to salinity, transcriptome profiling of mRNA expression was analyzed for 12 candidate genes in leaves, shoots, and roots of five Hernandina clementine scions grafted on Rangpur lime (LR), Volkamer lemon (CV), Carrizo citrange (CC), sour orange (Big), and Cleopatra mandarin (MC) rootstocks in response to moderate and severe salinity. qRT-PCR analysis revealed differential gene expression that varied by rootstock, salinity level, and tissue. The majority of induced genes were those involved in ion transporter proteins (mainly NHX1 and HKT1 genes), Cl− homeostasis (CCC1 gene), biosynthesis and accumulation of compatible osmolytes, proline (P5CS gene) and glycine betaine (CMO gene), accumulation of proteins (LEA2 gene), and ROS scavenging antioxidant activity (mainly APX). We show that these expression patterns could explain the relative tolerance of the used rootstocks and report new insights on the main salt tolerance mechanisms activated by these rootstocks.