Endogenous viruses exist in all kingdoms. They usually have active mechanisms of integration, as in bacteriophage lambda and animal retroviruses, and sophisticated mechanisms to maintain a proviral state over decades and generations. Plant para retroviruses, however, neither have an integrase, nor genes for maintaining the proviral state. How are those elements controlled, and under what conditions can they be activated? Here we study the proviral state of endogenous petunia vein clearing virus (ePVCV). Our results support the hypothesis that the proviral state is associated with a host silencing mechanism manifested by DNA methylation, chromatin modification and production of small interfering (si) RNAs. PVCV may be induced by applying abiotic stress, leading to the development of viral symptoms and increased transcript and siRNA levels. Similar levels of ePVCV DNA methylation were observed in two different lines of Petunia hybrida, RdC (rose du ciel) and W138, the latter known for its active version of transposon dTph1. In contrast, significant differences in histone modification were detected. The predominant association of ePVCV sequences with histone H3 methylated at lysine 9 (H3mK9) in RdC and with about equal amounts of H3mK9 and H3mK4 in W138 indicates a less repressive proviral state in the latter cultivar.