Floriculture has a large production value in Italy, with 30,000 hectares of plantation and more than 100 thousand employees. Abelia grandiflora and Lantana camara are two ornamental species cultivated for decorative purposes; however, unlike other crops, very few reports report the presence of viruses and viroid infections. Furthermore, the EU legislation includes Lantana and Abelia species, as well as many other species, in its certification program description. This situation necessitated an investigation to seek for known and unknown pathogens (viruses and viroids) infecting these species and for identifying healthy plants that could be used as candidate mother plant material for future certification program of ornamentals in Italy. PCR assays and High-Throughput Sequencing technology had identified 4 novel viruses belonging to Caulimoviridae, and Geminiviridae families, for which one full virus genome sequence was determined. None of the known viruses that infect these species have been detected in the surveyed samples except for apple chlorotic leaf spot virus found for the first time in Lantana species. 17 Lantana and 20 Abelia plants were found free of viral infections and can be used as a candidate plant material in the future certification program of ornamentals.