There are many non-pathogenic viruses that are maintained in a persistent lifestyle in plants. Plant persistent viruses are widespread, replicating in their hosts for many generations. The roles of plant persistent viruses have not been studied thoroughly, but their very long-term relationships with their hosts, and their high level of vertical transmission imply beneficial interactions. So far, Endornaviridae is the only family with a single-stranded RNA genome, containing one large open reading frame. Bell pepper endornavirus (BPEV), Hot pepper endornavirus, Capsicum frutescens endornavirus 1 (CFEV 1) have been identified from peppers. Peppers are native to Central and South America, and as domesticated plants human selection accelerated their evolution. Using a collection of 97 different peppers the evolution of pepper persistent viruses was studied. The evolution of endornaviruses in different peppers was investigated using two fragments from the viral helicase (Hel) and RNA dependent RNA polymerase (RdRp) domains. In addition, by using single nucleotide polymorphisms the pepper host populations and phylogenies were analyzed. The endornaviruses phylogeny was correlated with its Capsicum species host. In this study BPEV was limited to C. annuum species, and the RdRp and Hel phylogenies identified two clades that correlated with the host pungency. No C. annuum infected with CFEV 1 was found in this study, but the CFEV 1 RdRp fragment was recovered from C.chinense, C. frutescens, and C.bacccutum and C. pubescens.Partitiviridae is the most common persistent virus family in wild plants. Jalapeo and Hungarian Wax peppers (Capsicum annuum) have been reported with Pepper cryptic virus 1 (PCV 1) and Pepper cryptic virus 2 (PCV 2), respectively. Both viruses belong to the genus Deltapartitivirus from Partitiviridae family. The evolution of PCV 1 and PCV 2 was investigated using the RdRp and coat protein of both viruses. Both viruses were detected in cultivated and wild peppers. It is shown that these viruses have a remarkably slow evolution rate in comparison with acute RNA viruses. This might be correlated with the strong purifying selection related to the lifestyle of theses viruses, or the replication strategies in double stranded RNA viruses, that use a stamping machine mode of replication. Finally, some potential beneficial effects of persistent virus were examined. In wild plants partitivirus infection decreased the likelihood of acute virus infection. I compared the effect of odor cues from PCV 1 infected (J+) and virus free (J-) Jalapeo pepper on the aphid Myzus periscae, a common vector of acute plant viruses. Pairwise preference experiments showed a stark contrast to insect-plant interactions in acute virus infections: virus infected plants deterred aphids. The acute plant virus Cucumber mosaic virus (CMV) manipulates its host's volatile emission to attract aphid vectors and facilitate its transmission. Volatiles of J+ and J- CMV infected plants were more attractive to aphids than J+ and J- mock inoculated plants. However, in pairwise preference between J+ CMV- and J- CMV-infected plants, aphids preferred the J- CMV volatile blend. Also, aphid fecundity on J+ and J- plants was measured as an indicator for the effect of PCV 1 on host quality for aphids. Aphid reproduction on J+ plants was more than two fold lower than J- plants. This study demonstrates a beneficial relationship between PCV 1 and Jalapeo plants by protecting the plants from the vector of acute viruses. In addition, the effect of PCV 1 on the Jalapeo's developmental growth was tested by measuring the average time required for seed germination, emergence of first true leaf, first open flower and dried biomass of plants. PCV 1 showed no significant effect on the developmental growth of Jalapeo plants.