Kenaf is a fast growing important industrial crop and performs reasonably better under salt stress conditions. However, differences exist among kenaf genotypes for salt tolerance. To evaluate the influence of salt tolerance among seven alloplasmic kenaf materials, the present study was performed to identify the beneficial genetic variation of heterologous cytoplasm during germination and early seedling stages. The results showed that seed vigor, phenotypic characteristics and seedlings root growth of seven materials were substantially influenced by salt stress. The hybrids, C2/992, C3/992, and C4/992 showed better seed vigor, while C1/992 and the restorer lineFH992 were found sensitive to salt stress. NaCl concentration was negatively correlated seedling growth. Seedling height, aboveground fresh weight, SPAD, and root growth were significantly reduced withincreasing salt stress. The hybrids C4/992 and P3B were found better in root growth as compared to C2/992 and FH992. Moreover, four isonuclear alloplasmic cytoplasms exhibited differential cytoplasmic effects on same or different traits both at germination and seedling stages. Taken together, C4 cytoplasm has more positive effects on seed vigor and seedling growth under salt stress than others cytoplasm and hence its cultivation under saline conditions is suggested. P3A, as a female parent, could be used for salt tolerance breeding.