Microbial endophytes are integral factors in plant evolution, ecology, and physiology. However, the endophyte communities across all major plant lineages have yet to be characterized, and data are particularly scarce for lycophytes. Here we used a culture-based approach to survey the diversity of endophytic bacteria in five sympatric Lycopodiaceae species in central New York. The most notable endophyte isolated from this study is a bacterial species Allobranchiibius huperziae, which was only recently described from the roots of Huperzia serrata in China. The fact that the same endophyte was also found in our North American samples suggest a possible specific association with Lycopodiaceae species. The data and cultures from this study provide an important foundation for future metagenomic and functional studies to characterize better the diversity and significance of plant endophytes.