A two-season study evaluated five microbes in the nematode community associated with citrus trees under field conditions in Egypt. These microbes were Trichoderma asperellum, T. harzianum, two strains of the bacteria Pseudomonas fluorescens, and the yeast Rhodosporidium paludigenum, and the last was not previously studied against plant parasitic nematodes (PPNs). All the tested microbes decreased the number of PPNs under field conditions by the time after application. In addition, R. paludigenum was the most effective against the citrus nematode Tylenchulus semipenetrans. The reduction percentage in J2s numbers was 59.5 and 60.7% after four weeks of application in the first and second seasons, respectively, while P. fluorescens race1 was the most effective against Xiphinema spp., with a recorded reduction 75.7 and 77.7% after the same application period in the first and second seasons, successively. On the contrary, no suppressive effect was recorded for the tested microbes on non-target nematodes (NTNs), and their numbers were increased. For example, the Tylenchus number increased in R. paludigenum application by 52.7% after four weeks of application in the second season. In contrast, Dorylaimus, Mononchus, and free-living nematodes increased by 69.9, 86.3 and 71.8% in T. asperellum application, sequentially, after four weeks of application. On the other hand, the effect of these tested microbes was investigated on T.semipenetrans under lab conditions to confirm the effect on J2s activity and eggs hatching. The obtained results were in harmony with the field study. This study aims to investigate the effect of previously tested microbes on beneficial nematodes associated with citrus trees and confirm their biological control role against PPNs with a focus on the promising biocontrol agent (R. paludigenum), which was not tested before comprehensively on the nematode community.