The effects of salinization with 40 mM sodium chloride on P. trifoliata (L.) Raf., C. grandis (L.) Osb. and their F-1, and a BC, progeny population [C. grandis x (C. grandis x P. trifoliata)] were investigated. A total of 272 traits were analyzed in salinized and non-salinized BC1 progeny, including parameters of growth, tissue and whole plant dry mass accumulations, and tissue and whole plant accumulations and interactions of 11 macro and micro elements. The comparison of the three parental types to the BC, progeny under control and saline conditions showed that the BC, progeny plants segregated transgressively for many traits. Many putative quantitative trait loci (PQTLs) were located to the previously generated linkage map with LOD scores greater than or equal to 3.0. Important genomic regions involved in different aspects of salinity were identified by considering LOD scores, map locations, and correlation analyses of the traits. Correlation analyses and locations of PQTLs indicated that many traits were controlled by fewer genes than the actual number of QTLs mapped within the same region e.g., totals of 58 and 22 PQTLs mapped in clusters at the beginning of two different linkage groups for accumulation of and/or interaction between K, Na, and/or Cl related traits. This is the first step in identifying QTLs that may have a major impact on salinity tolerance in Citrus and the implications of these findings will be discussed.