DNA methylation as epigenetic mark plays a key role in normal differential and developmental processes as well as in dynamic gene regulation at the genomic level. To assess DNA methylation pattern in different developmental stages of Aeluropus littoralis, methylation sensitive amplified polymorphism (MSAP) was used. Methylation and demethylation status at the CCGG recognition site were tracked by two sets of cytosine methylation-sensitive enzymes (MspI and HpaII), which were classified into three types. The percentage of total bands per type I (non methylation), type II (CpG methylation) and type III (CpCpG methylation) fragments were 75.7, 19.4 and 4.9, respectively. The most frequent methylation events (19.4%) were observed in type II fragment in which full methylation pattern occurred. Out of 480 bands, 33 bands showed methylation alterations between differential developmental stages in all three types of detectable methylation levels. In this study, polymorphic bands had two main directions associated with methylation or demethylation patterns in which methylation level increased during plant development. The methylation and demethylation events at CG sites could be related to developmental stage-specific gene regulation.