Nematode infection of plant roots is a paradigm of host parasite interactions. Although nematodes can be labeled with fluorescent dyes, migration of the worms into the deep regions of host roots makes them difficult to track. Here we report the use of two fluorescent dyes, FM4-64 and SYBR green I, to intensely label the soybean cyst nematode (SCN) Heterodera glycines for one week in host plants. Continuous monitoring of the labeled SCN juveniles was achieved with two-photon microscopy. Additionally, we developed a transient transformation system consisting of the non-model leguminous plant (fabaceous) roots, Astragalus sinicus and Agrobacterium rhizogenes to observe the cellular structures of the plant during SCN infection. By the combined use of fluorescent dyes and two-photon microscopy, clear images of infecting SCNs were obtained even in deep regions of A. sinicus roots. The fluorescent labeling described herein can also be used in detailed monitoring of the infection processes of other non-model nematodes, as well as the associated morphological changes in the host plant roots.