The entomopathogenic nematode Steinernema carpocapsae is mutualistically associated with the bacterium Xenorhabdus nematophila. Infective Juveniles (IJs) transport X. nematophila cells that provide them with good conditions to reproduce within the insect. In the laboratory, long term stationary-phase culture conditions sometimes lead X. nematophila's variant 1 cells, which were previously isolated from the worms, to spontaneously and irreversibly change into a new phenotypic variant (variant 2). In this paper, we tested the ability of each phenotypic variant to (i) be transmitted by IJs, (ii) to optimize the worm's fitness within the insect, and (iii) to counteract the effect of closely related antagonistic bacteria previously shown as being able to totally prevent S. carpocapsae's reproduction within the insect. We found that IJs did associate with cells of both phenotypes but that the variant 2 cells were preferentially retained by the nematodes when both variants were present in the insect. Both phenotypic variants led to the same fitness of S. carpocapsae in insects not infected by antagonistic bacteria. In insects infected by antagonistic bacteria, both variants were able to provide protection to S. carpocapsae. Nevertheless, this protection depended on the phenotypic variant and the antagonistic bacteria that were co-injected into the insect. Further analysis conduced in vitro showed that this variability could be partly linked to the sensitivity of each antagonistic bacterium to xenorhabdicin, produced by X. nematophila.