There is a growing number of plant genomes that are being sequenced, but most of these available assemblies do not cover the entire genome mainly due to the highly repetitive sequences found in most plant genomes. Nevertheless, these repeats, although a challenge in assembly algorithms, provide relevant information about a genome’s history that could help explain its structure and complexity. Here, we cytogenetically mapped previously and presently characterized major repeats of Panax ginseng genome, including several LTR retrotransposons (PgDel2, PgDel3, PgTat1, PgTat2, PgTork) and one tandem repeat, PgTR Fluorescence in situ hybridization (FISH) results showed differential accumulation of Ty3/gypsy LTR retrotransposons into different chromosomal regions or subgenomes, suggesting a non-random preferential amplification of retrotransposons in these regions and an allopolyploid origin of P. ginseng. In silico analysis based on 1x whole genome sequence reads suggests that PgTR is the most abundant tandem repeat in ginseng, which was further corroborated by FISH analysis. More importantly, its unique distribution pattern among the 24 ginseng chromosomes, coupled with the non-random distribution of LTR retrotransposons and rDNA arrays, allowed us to discriminate and characterize each individual ginseng chromosome. These different newly characterized cytogenetic markers allowed reorganization of previously reported ginseng karyotype with better resolution, demonstrating the irutility in ginseng chromosome identification. These information give us insight about the genomic structure of P. ginseng, and should be useful for future comparative cytogenetics studies among closely related species to unravel its genomic history. This work was supported by the Next-Generation BioGreen21 Program (No. PJ008202), Rural Development Administration, Republic of Korea.