Camptotheca acuminata Decne (Nyssaceae) is a well-known ornamental. It is also a major natural source for the monoterpene-indole alkaloids camptothecin (CPT) and 10-hydroxycamptothecin (HCPT). Salinity is one of the major constraints to agricultural production. In order to develop salt tolerant C. acuminata lines, we analyzed the effect of NaCl stress and DNA methylation level by ISSR. In this study, we sought to explore a possible relationship between NaCl stress and DNA methylation in C. acuminata as salinity affects many areas around the world. Results showed that NaCl stress significantly affected shoot proliferation and rooting on WPM. The effects of low concentration of NaCl (30 mmol l^-1) on the proliferation coefficient and rooting percentage were significantly higher when compared to the higher NaCl concentrations (45 to 120 mmol l^-1). The highest shoot proliferation coefficient and rooting percentage were 6.26 and 80.7%, respectively. ISSR analyses showed that there is a negative correlation between the NaCl concentration and the DNA methylation level in shoot proliferation and rooting. Low NaCl concentration (30 mmol l^-1) can maintain leaves at a high methylation level in proliferation (16%) and rooting (5.2%), while under the higher NaCl concentrations (45 to 120 mmol l^-1), the methylation level decreased and the seedlings growth declined dramatically.