AbstractBACKGROUNDPhelipanche aegyptiaca is one of the most noxious parasitic weedy broomrapes in Xinjiang, China. Understanding its morphological polymorphism and genetic diversity can support effective control strategies. This study investigated the morphological and genetic diversity among and within populations from different geographical regions and host species across Xinjiang to characterize their relationships.RESULTSThirteen ISSR primers were used, resulting in 173 clear bands, 172 of which (99%) were polymorphic. Significant genetic variations were observed within regional and host groups, while variation among groups was relatively low. Gene flow was frequent, with a significant correlation of 1.57 between geographic regions and 5.57 between host species groups. Morphological traits exhibited substantial variability, with diverse coefficients ranging from 16% to 50%. Canonical correspondence analysis indicated that samples primarily clustered by region, not by host species. There was a significant correlation between morphological and genetic diversity across geographical groups.CONCLUSIONThe findings suggest that genetic and morphological diversity are key factors in the expansion of P. aegyptiaca's host‐range and its spread. Morphological diversity appears to result from the interaction between genetic variation and environmental factors. This study offers new insights into the adaptation and evolution of P. aegyptiaca in relation to its genetic, morphological diversity and dissemination. © 2024 Society of Chemical Industry.