In recent years, orange trees exhibiting declining, general yellowing, leaf stunting, mottling and yellowing with green veins, were observed in different areas of southern Kerman province. In these trees, the fruits occasionally were small, lopsided with colour inversion and aborted seeds. These symptoms were similar to those described for citrus huanglongbing ( Candidatus Liberibacter .) and stubborn ( Spiroplasma citri ) diseases. As a result of these similarities and widespread presence of phytoplasma-induced diseases in the region, the possibility of orange trees being infected with one or more of these pathogens in the area is not too far-fetched. Because of the correspondence of symptoms between HLB and stubborn disease and misdiagnosing the type of the infection of these trees by observation, and also due to the economic importance of the declining of the orange trees, this research tries to determine the possible occurrence rate of each of the pathogenic agents HLB, stubborn and phytoplasma in the orange trees of southern Kerman. To this end, during the years 2012 to 2014, a significant number of leaf and fruit samples from orange trees with yellowing and declining symptoms were collected from Arzueieh, Jiroft, Faryab and Kahnooj areas. After DNA extraction from leaf midribs and columella of the samples, the detection of Ca . Liberibacter ., S.citri and phytoplasma performed by PCR technique, using general and specific primer pairs. Primer pairs OI1/OI2c were used to detect HLB disease in PCR reaction which led to amplification of 1160 bp DNA fragment in some samples. Digestion of the fragment obtained from different samples with restriction enzyme XbaI yielded two bands 520 bp and 640 bp showing that all strains belong to Ca . Liberibacter asiaticus ( LAS ).The nucleotide sequence analysis of this fragment also revealed its high similarity (99%) to Ca . Liberibacter asiaticus. Using LAMP method with rpl and Las primers led to detection Ca . Liberibacter asiaticus efficiently and specifically in infected samples. In order to detect stubborn disease in orange samples, primer pairs Spiralin-f/r, P58-6f/4r and P89-f/r were used in the PCR analysis; however, the detection of stubborn disease was not successful with the primer sets in this study. In 102 assessed samples, no band was produced with Spiralin-f/r but the expected band as well as some non-specific bands were produced with primer pairs P58-6f/4r and P89-f/r, although the nucleotide sequence analysis of the fragments showed that the mentioned fragments do not bear any resemblance to spiroplasma and therefore no spiroplasma agents were detected in the investigated orange trees. Probably collection of samples in autumn and winter, when pathogen concentration in host plant is low, is one of the reasons for not tracking the stubborn. To determine phytoplasma associated with orange samples, primer pairs P1/P7, P1A/P7A and R16F2n/R16R2 were used in PCR and Nested-PCR reactions. Based on the results the Nested-PCR using P1A/P7A followed by R16F2n/ R16F2n/R16R2 was considered as a sensitive method for the detection of phytoplasmas in diseased trees. To determine the diversity of phytoplasma groups with orange samples, DNA fragments amplified by primer pair R16F2n / R16R2 were digested with restriction enzymes RsaI , TaqI and HhaI ( CfoI ). The result related to the RsaI digestion showed that two different groups of phytoplasmas influence the infection of orange trees. Comparing the nucleotide sequences of some strains related to these two groups of phytoplasmas led to the identification of Stolbur and Clover proliferation groups as phaytoplasmas associated with orange trees. So far, no reports have confirmed the existence of these phaytoplasmas in orange trees. Applying specific primer pairs Ast-F / m2Sol-R and TRF2-F / TRF-R, respectively for Stolbur and Clover proliferation groups, confirmed the association of both phytoplasma groups separately and simultaneously, and also the abundance of phaytoplasmas Stolbur group was relatively more in the area.The results showed that, in combination or separately, there is a risk of being infected with HLB for orange trees, phytoplasmas Stolbur group and Clover proliferation group with similar symptoms on orange trees in the south of Kerman. However, samples of oranges infected with stubborn and witches' broom diseases were not detected. Key Words: C andidatus Liberibacter asiaticus, Spiroplasma citri , Stolbur group , Clover proliferation group‌, Phytoplasma