[Objective] The aim of the study is to investigate whether the environmental DNA (eDNA) of Casuarina equisetifolia protective forests inhibits seed germination and seedling growth of C. equisetifolia, thereby providing a theoretical basis for natural forest regeneration in the understory. [Methods] We used C. equisetifolia seeds as the research subject and extracted DNA extractions from fresh leaves of three distinct plants: C. equisetifolia, Acacia formosana, and Pinus elliottii. Subsequently, we prepared extraction solutions with concentrations of 0.01, 0.1, and 0.5 g/mL, as well as DNA extraction solutions with concentrations of 20, 200, and 2000 μg/mL. Additionally, we used DNA solutions from the three types of fresh leaves at a concentration of 2000 μg/mL to which an equal volume of DNaseΙ was added for degradation treatment. [Results] (1) The 0.1 g/ml extract of C. equisetifolia leaves inhibited seed germination, with the inhibitory effect increasing with concentration. The 0.5 g/mL concentration was identified as the threshold for allelopathic substances limiting seed germination, showing a low-concentration promotion and high-concentration inhibition effect. (2) High concentrations of self-derived eDNA significantly inhibited both seed germination and seedling growth of C. equisetifolia. A concentration of 2000 μg/mL of leaf DNA solution is likely the threshold for eDNA autotoxicity on seeds and seedlings. (3) Non-self eDNA had no significant effect on seed germination of C. equisetifolia. Both allelopathic autotoxic substances and self-derived eDNA caused significantly greater damage to seedling roots than to stems and leaves. [Conclusion] The germination of C. equisetifolia seeds and the subsequent growth of seedlings are markedly influenced by autotoxicity and elevated levels of endogenous DNA, resulting in the inhibition of natural regeneration within C. equisetifolia forests.