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In this study, cyan fluorescent protein (cfp) labeled endophytic rhizobia of Dolichos lablab L. was used as the test strains which had strong nitrogen-fixing ability, low fluorescence loss rate, and good genetic stability. Through methods such as reinoculation and spot application of bacterial suspension in rocky desert mountain areas, we investigated the quantity and distribution of fluorescently labeled rhizobia in Dolichos lablab L. plants at different growth stages, as well as the migration characteristics of these bacteria on the surface of rocky desertified soil in the absence of hosts. The results indicate that in terms of spatial distribution, the fluorescently labeled rhizobia concentrated in the roots primarily. Specifically, during the vegetative stage, they are mainly present in the taproot, while from the budding stage to the pod-setting stage, they are predominantly found in the lateral roots. In terms of temporal dynamics, the highest count during the vegetative stage and the lowest during the budding stage. The number of labeled bacteria in the aboveground part of the plant was only 39.93% of that in the root, mainly distributed in the stem tip, flower bud and pod. During the development from flower buds to pods, the quantity of labeled bacteria shows a trend of increase-decrease-increase, with the lowest count observed inside the flowers. The surface soil of rocky desertification provides a suitable microenvironment for the survival of fluorescently labeled rhizobia. These labeled rhizobia can colonize the surface soil of rocky desertification and migrate across the soil surface over time. They can migrate from the central po int O in vertical, oblique, and horizontal directions, but their distribution at various sampling points is discontinuous and unstable.