Structural Variations (SVs) regroup very diverse genomic rearrangements (with a length often more than 50bp). Their identification remains in infancy in plants mainly due to the limited useful genomic resources. Today, last technologies based on long DNA fragments offer new possibilities to identify such polymorphisms. In our study, long-read sequencing obtained with the MinION instrument (Oxford Nanopore Technologies (ONT)) and optical maps produced by the Saphyr device (BioNano Genomics), were evaluated on their ability to identify SVs between two Arabidopsis thaliana ecotypes, Columbia-0 (Col-0) and Landsberg erecta-1 (Ler-1). Corrected and trimmed Col-0 and Ler-1 ONT sequences were assembled with SMARTdenovo. MUMmer tools were used to align the assemblies on public references of each ecotype and for the SVs detection. In parallel, we used the BioNano SV detection tool which identifies the SVs by comparing the maps obtained with the DLE-1 enzyme with the in silico digested reference genome maps. The ONT and BioNano SVs were considered as the same if their absolute positions overlapped. For all the comparisons performed in our study, more than 90% of BioNano SVs were detected with ONT and ~70% of ONT SVs were obtained with BioNano. However, The SV > 1000b were identified by both technologies. ONT SVs were smaller and less reliable in complex region whereas BioNano SVs were longer with more confidence. Challenges on wet lab part, in particular extraction of high molecular weight DNA, are still relevant.