Alabama historically supported the most species-rich freshwater mussel fauna in North America.  Now, many formerly species-rich streams support only relict populations.  Species that persist at very low densities present significant challenges to sampling protocol design.  Sampling protocols need to be sensitive enough to find rare species and also need to provide rigorous estimates of abundance so managers can track population trends.  We sampled mussels at 22 sites across Alabama in 2006 and 2007 using both timed searches and quadrat sampling.  After each 150-m reach was surveyed using timed searches, we excavated 75 one-quarter m2 quadrats at 10-m intervals.  Timed searches consistently yielded more total taxa than quadrats suggesting that our quadrat-sampling frequency was insufficient to adequately characterize mussel diversity in sites with >8 mussel species.  However, species richness estimates derived using qualitative and quantitative methods were more similar in streams with higher Shannon diversity index scores than in streams with lower index scores.  These data suggest that timed searches may be more applicable for surveys of multiple at-risk taxa in streams supporting a large number of low-density mussel populations.  However, more limited quantitative sampling regimes may be sufficient to characterize low diversity, high-density mussel assemblages.