Macroinvertebrates in the Prairie Pothole region of the United States have been poorly studied.  Littoral habitats often harbor great invertebrate diversity and production in lentic ecosystems.  The objective of this analysis was to describe and compare littoral invertebrate communities of macrophyte beds and rocky shoreline habitats.  These two habitats may comprise up to 90% of pothole shoreline habitat.  Ten plots were constructed in each habitat type and invertebrates were sampled three times from late June to middle July during the summers of 2006 and 2007.  A 300-count subsample was sorted and identified to lowest practical taxonomic level.  Jaccard similarity between habitat types was 45%.  Macrophytic habitats had significantly higher percentages of Insecta, Chironomidae, collector-gatherers, and Ephermeroptera, Trichoptera, and Odonata.  Rocky habitats had significantly higher percentages of predators (ANOVA p>0.05).  Percent tolerant taxa (tolerance values ≥7.0) were lower in rocky shore habitats than macrophyte beds but not significantly (p=0.07).  Results of this effort suggest different taxonomic composition and guild structure between macrophytic and rocky littoral habitats.  Within lake variation in community composition, guild structure and tolerance must be considered in the context of future monitoring and assessment efforts.