DNA methylation is an epigenetic modification that has the ability to alter gene expression without any change in the DNA sequence. DNA methylation occurs when a methyl chemical group attaches to cytosine bases on the DNA sequence. In mammals, DNA methylation primarily occurs at CG sites, when a cytosine is followed by a guanine in the DNA sequence. In plants, DNA methylation can also occur when a cytosine and a guanine are separated by any of the other three bases (CHG sites) and also when neither of the two bases following a cytosine are guanine (CHH sites). Whole-genome bisulfite sequencing studies enable researchers to measure methylation levels across the whole genome and make comparisons between different conditions. Many of the statistical methods that have been developed to estimate methylation levels and test differential methylation incorporate the observed correlation between methylation levels of neighboring cytosine sites. However, most of these methods have been applied to human studies, where only CG sites are investigated. In this study, we focus on plant studies and show that the correlation between methylation levels at neighboring sites differs between the different methylation contexts that occur in plants. We investigate the importance of accounting for the methylation context in the correlation structure by comparing the performance of three existing methods (MethylSig, MAGI, and M3D) both with and without considering the methylation context.