The Chinese jujube (Ziziphus jujuba Mill.) is a fruit crop originating from China and of growing economic interest in Italy. Due to the lack of information available on the health status of this species, a comprehensive survey was conducted to assess the presence of viruses and viroids infecting jujube trees in the Apulia region (southern Italy). Leaf samples were collected from 120 jujube trees, all apparently asymptomatic, whose total nucleic acid extracts were used for PCR analysis using specific primers found in the literature. None of the jujube-infecting viruses and viroids known to date, i.e., jujube mosaic-associated badnavirus (JMaV), jujube yellow mottle-associated emaravirus (JYMaV), persimmon ampelovirus jujube (PAmp-Ju), and hop stunt viroid (HpSVd), was detected in any of the samples analyzed. Next-generation sequencing (NGS) performed on a pool of nucleic acid extracts representative of all collected jujube samples showed the presence of large contigs whose genomic sequences were highly identical to the turnip yellow mosaic virus (TYMV) in the BLAST analysis. RT-PCR analysis, using specific primers designed on the CP region, detected TYMV in 4 out of 120 tested jujube samples (3.3%). After the sequence genome alignment with other TYMV isolates and the design of new primers to close the gaps between the contigs, the complete genome sequence of TYMV-Ju isolate was determined, which showed a nucleotide identity with other TYMV isolates available in GenBank ranging from 89.9% to 96.3%.