pldist allows distance-based analysis of paired and longitudinal microbiome data. In particular, the package supports both paired and longitudinal versions of unweighted UniFrac, generalized UniFrac, Bray-Curtis, Jaccard, Gower, and Kulczynski distances or dissimilarities. Functions implementing the transformations that underlie these distances are also provided so that transformed OTU data may be included in analyses beyond distance-based methods. The code can handle paired data, balanced longitudinal data, and unbalanced longitudinal data, although use for highly unbalanced designs is not recommended.