Chloroplast DNA is methylated in the kelp Saccharina japonica, in contrast to most plants. Its function is yet largely unexplored. We detected methylation in the chloroplast DNA of the congener Saccharina latissima, a non – model macroalgal species of high ecological (wild populations) and economical (wild and cultured populations) importance in the North Atlantic. To the functional relevance of chloroplast DNA methylation, we compared for the first time methylation patterns between wild and cultured kelp from different climatic regions (High-Arctic (79 °N) and temperate (53 °N), laboratory samples at 5 °C, 10 °C and 15 °C). Our results suggest genome –wide differences in methylated sites, and methylation level, between the climatic regions. At gene level, our data found functions related to photosynthesis to be the predominant affected case only for differential methylation between origins, but not between growth conditions. Here, sample origin led to significant differences between cultivated and wild samples due to differential methylation of genes related to DNA replication in the Spitsbergen samples. Both findings indicate that origin and cultivation strongly affected the chloroplast methylome, but differently. Similar methylomes for samples from the same origin — independent from whether they grow in the wild or in the lab — suggest that origin– specific methylation marks on the chloroplast genome are inherited. However, the capacity for rapid adaptation (to cultivation conditions) could be shown for Saccharina latissima during this study. Given that DNA – methylation affects gene expression, our study suggests that lab – cultivation alters epigenetically determined kelp chloroplast characteristics at least to the same degree as ecotypic differentiation does.