RESUMO
<p><b>OBJECTIVE</b>A total of 27 samples belonging to 5 cultivars of Fructus Aurantii (Citrus aurantium), i. e. cv. Xiucheng, cv. Xiangcheng, cv. Lecheng, cv. Jizicheng, and cv. Youzicheng, collected at Changfu and Huanggang, Zhangshu City, Jiangxi Province, were assayed to reveal the genetic relationship among the cultivars and the accordance between morphological and molecular markers.</p><p><b>METHOD</b>Cultivar identification was based on morphology and cultivar relationship was based on Inter-simple sequence repeats (ISSR).</p><p><b>RESULT</b>Twenty out of 40 ISSR primers screened generated 392 loci across all 27 samples with 315 informative loci. The UPGMA dendrogram showed that samples within cv. Xiucheng and cv. Xiangcheng from Changfu were closely related. However, samples of cv. Lecheng, cv. Jizicheng and cv. Youzicheng from Huanggang, or cv. Xiucheng and cv. Xiangcheng from both Changfu and Huanggang did not exhibited close relationships within each cultivars.</p><p><b>CONCLUSION</b>Based on morphology the same cultivar grown in different plantations, or even within a single plantation sometimes do not show close genetic relationship, indicating diverse origin of the cultivars. Synonyms or homonyms are believed to common phenomenon in Fructus Aurantii production. To solve the problem ISSR markers can serve a kind of molecular markers which are preferable to partition genetic variations within and between cultivars and to establish genetic relationships among them.</p>