Background: Repetitive elements (REs) or repeats are sequences that occur multiple times in the genome. They represent a significant part of the gigantic conifer genomes (70-80%) relative to mammals and other plants and complicate whole genome sequencing and annotation. However, REs play important roles in evolution and adaptation processes in both plants and animals. Moreover, amino acid repeats play an important role in plant immunity being a structural element of the products of some disease resistance genes. Analysis of REs in conifer genomes is an important fundamental task.Results: REs were identified de novo and partly classified in the Siberian larch (Larix sibirica Ledeb.) nuclear genome for the first time. In total, 20.9 million REs were detected with the total size of 4.8 Gbp, which comprises about 39% of the 12.3 Gbp larch genome. Resistance genes with leucine-rich repeats (LRRs) were also identified and analyzed in the transcriptome data of autumn buds obtained using RNA-seq.Conclusions: For the first time, REs were identified and classified in the Siberian larch genome and transcriptome. In addition, LRRs and resistance genes were identified and analyzed in the Siberian larch transcriptomes from autumn buds. The larch genome contains twice as less RE compared to other conifers in the same Pinaceae family (39 vs 70-80%), and it might explain why it also has almost twice as smaller genome size (12 vs 18-31 Gbp).