The sequenced genome data of the sea urchin Strongylocentrotus purpuratus were used to identify transposons (TEs, transposable elements) and test for the presence of some of them in the genome of the sea urchin S. intermedius. The known TEs of S. purpuratus from the RepBase repeats database were used to calculate the primers and identify the corresponding TEs in the S. intermedius transcriptome. High-coverage TE sequences from the S. intermedius transcriptome were assembled based on comparison with the annotated TEs of the S. purpuratus genome. TEs with an insufficient number of reads in the transcriptome were beyond the analysis. The approach applied in the present study was successful: out of the 100 assembled TEs of S. intermedius, 92 corresponding TEs in the S. intermedius genome were identified using the calculated primer pairs. The TE sequences calculated by in silico methods are present in the S. intermedius genome and can be useful in further research.