Lettuce (Lactuca sativa L.) is widely planted and considered a valuable crop in Iraq. Next generation technology (NGS) and bioinformatics analysis were used to detect endogenous Para retroviruses in the genome of lettuce. In this study, two virus elements were identified, belong to two genera, Caulimovirus and Florendovirus, which were named Caulimovirus-LSa, and LsatiV respectively. The full length of Caulimovirus-LSa, and LsatiV were 7827, 7205 bp respectively. The Caulimovirus-LSa encodes seven coding domains; movement protein (MP), Cauli-AT, Cauli-DNA-bind, Peptidase-A3, RT-LTR, RNase-H and RT-RH. The LsatiV has five domains of RNaseH (RH), RT-RH, reverse transcriptase (RT and RVT) and movement protein (MP). Interestingly the sequence of LsatiV was inverted from 3' to 5', unlike Caulimovirus-LSa. Transcripts per million values (TPM) were 4.3 and 4.45 for Caulimovirus-LSa, and LsatiV respectively, which considered low in expression. However, the resemblance of almost 60% between Peptidase, RT and RH domains of Dahlia mosaic virus (DMV) and Caulimovirus-LSa probably indicate co-infection alongside pathogenic virus or viroid agents that might be caused symptoms in lettuce. The phylogenetic tree confirms the close relationships of both viruses to endogenous viruses from Taraxacum officinale that belong interestingly to the same family Astraceae.