A survey was conducted to assess the phytosanitary status of Viburnum and Bougainvillea plants in six ornamental plant nurseries in Apulia region. A total of 117 samples (59 Viburnum and 58 Bougainvillea) were analyzed by RT-PCR against all known viruses and viroids for these species (BCVBV, INSV, TYRSV, ClYMV, CMV and HSVd for Bougainvillea, and AMV, SDV, TRSV and HSVd for Viburnum). Only AMV was detected in 25.4% of the Viburnum samples, and, for the first time in Italy, BCVBV in 8.6% of the Bougainvillea samples. The HTS was also applied to two pools of 20 PCR-negative samples for each of the two species. In the Bougainvillea samples, this technique revealed the presence of at least two BCVBV isolates, whose complete genome sequence was determined. These two Italian isolates showed the highest identity in BLASTn with isolates of Malaysian BCVBV-UKM (97%) and Brazilian BCVBV-UNB-01 (80%), respectively. For the latter virus, a specific primer set was designed that allowed detection of the BCVBV-UNB-01-like isolate in other 7 out of 58 (12.1%) Bougainvillea samples. The HTS also revealed the presence in Bougainvillea of another new viral entity of the family Caulimoviridae, genus Soymovirus, whose sequencing is currently being completed. A specific primer set designed in the reverse transcriptase region allowed the presence of this new virus, for which the name of Bougainvillea Soymovirus 1 was proposed, to be detected in 13.8% of the plants.