The present invention relates to nucleic acid molecules found in the genome of the Citrus Leprosis Virus (CiLV), which is associated to Citrus Leprosis (CiL) disease. The cloned CiLV nucleic acid molecules can be used as probes or can be used to design oligonucleotide primers useful in assays, such as a polymerase chain reaction, for detecting the presence of CiLV in biological samples, particularly leaves, roots and other tissues or organs of plants, such as plants from the genera Citrus and Poncirus. The invention comprises introducing the mentioned nucleic acid molecules in cloning vectors and cloning the recombinant nucleic acid molecules in cells, such as prokaryotes (e.g., bacteria like E. coli), and eukaryotes (e.g., yeast, COS, CHO, and other cells). The cloned CiLV nucleic acid molecules are expressed in cells to provide immunogenic proteins which can be used to raise antibodies against the CiLV, which can then be used to detect the presence of the CiLV virus in biological samples. It also comprises the nucleic acid molecules represented in SEQ ID Nos. 5 and 8, in whole or part, as well as transgenic plants, such as monocots and dicots, containing the CiLV nucleic acid molecules, in any kind of combination, so that expression increases resistance to CiL disease.