The structure of junction between inverted repeat (IR) and small single copy (SSC) regions of chloroplast genome in the representatives of non-core Caryophyllales is investigated in this work. It was found that for two families - Polygonaceae and Plumbaginaceae - the extension of inverted region is characteristic. This extension is due to the duplication the part of ycf1 gene that is partly located in the small single copy region in plants with typical structure of IR/SSC junctions. Comparison of the position of IR/SSC junctions in different species of Polygonaceae has shown that their exact position is not correlated with the affinity of these species inferred from molecular and morphological data. Possible mechanisms leading to the change in position of IR/SSC junctions observed in this work are discussed.