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Relict plants, remnants of Tertiary flora, survived geochronological ages, however, studies intended to ascertain the background of their fungal symbionts are limited. Different from many other relict plants, Gymnocarpos przewalskii Maxim. inhabits arid deserts region, mainly distributed in northwest China. In order to inquire the arbuscular mycorrhizal fungi (AMF) associated to G. przewalskii and their ecological significance in desert ecosystems, the seasonal dynamics of AMF and glomalin were surveyed in Anxi and Minqin in Gansu Province, northwest China. Soil samples in the rhizosphere of G. przewalskii were collected in July, September and December 2019, respectively. In total, 41 and 46 AMF species were identified via morphological techniques in Anxi and Minqin, respectively. Meanwhile, high throughput sequencing (HTS) data diagnosed 29 and 61 AMF OTUs in Anxi and Minqin, respectively. Glomus was the dominant genus in different seasons and locations in both morphological investigation and HTS data. AMF colonization (44.67–75.30%) and spore densities (19–248 per 20 g soil) varied sharply among seasons and locations. AMF colonization and spore densities showed significant positive correlations to most edaphic factors, except soil carbon: nitrogen ratio. Glomalin-related soil protein (GRSP) dramatically contributed to local soil carbon pool (51.54% in Anxi, 40.37% in Minqin), and the GRSP contents in soil were significantly affected by soil properties, season, and location. Random forest analysis indicated that soil humidity and total GRSP were the main factors shaping AMF communities. Our results showed that AMF colonization, spore density, and species diversity were higher and AMF community composition was less variable in Minqin where the soil nutrition levels were lower, which emphasized the necessity of AMF symbiosis for plants in harsh environments. The present research demonstrated the seasonal dynamics of soil AMF communities and glomalin and determined influential environmental factors in desert ecosystems. Our findings provide novel views on desert soil resource management and relict plant protection from an aspect of plant-AMF symbiosis. • Gymnocarpos przewalskii is a typical relict plant in the desert region of northwest China. • The colonization and structure of AMF have obvious seasonal and location heterogeneity. • Glomus spp. dominated AMF communities in desert soil across all seasons. • Glomalin might be useful indicators for evaluating soil quality and desertification. • Seasonal and location changes drive specific soil properties affected AMF community. [ABSTRACT FROM AUTHOR]