As part of a project on the evaluation of agricultural journals in the Iranian Academy of Sciences, the objective of this study was evaluation of quality of plant protection-related papers and management aspects of the journals publishing these papers in Iran. Ten indices were designed for evaluating the quality of published papers and another 10 indices for evaluation of the editorial quality of the journals. These indices were applied to 22 available journals published in 2014. The data were statistically analyzed using “normal distribution” procedure to rank the journals in 5 categories from “very good” to “very weak”. According to the results, 22.7‌‌% of the journals ranked “very good” or “good”, 54.6‌‌% were “intermediate”, and 22.7‌‌% ranked “weak” or “very weak”. The journals were also compared for five important indexes related to innovativeness, applicability and up-to-dateness of articles and practical usefulness and necessity of publication of the journal. Among the journals evaluated, Iranian Journal of Plant Pathology scored high in all 5 indices.  Other journals were significant by 4 indices (Journal of Entomological Society of Iran), 3 indices (Rostaniha), 2 indices (JAST and Persian Journal of Acarology), or one index (Mycologia Iranica, Iranian Journal of Virology, Applied Entomology and Phytopathology, and Plant Protection of Shahid Chamran University of Ahvaz). Other journals did not rank high in any index. It is recommended that 1- journals put more emphasis on the quality of papers, 2- very weak journals discontinue publication, and 3- more support be given to the journals sponsored by the scientific societies.