Plant roots host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, potential interactions and underlying mechanisms remain largely unknown in root-associated microbial communities at a continuous fine-scale. We analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment with more dense co-occurrences in bacterial-fungal network than in bacterial or fungal network, which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. Also, high abundances of genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH and lasR) and aerobic cobamide biosynthesis (cobG, cobF and cobA) were detected in the endosphere. Our results reveal intensified bacterial-fungal associations in the mangrove root endophytes, creating a distinct micro-environment to promote a biofilm life-style.