AbstractAutonomous recording units (ARUs) paired with signal classification software can be used to detect species‐specific calls, making them useful for evaluating patterns in avian occurrence and activity. However, classification of target signals is not always reliable and may be especially challenging for species that vocalize infrequently. We assessed the use of ARUs to identify and monitor habitat for a cryptic and federally threatened distinct population segment, the western yellow‐billed cuckoo (Coccyzus americanus) in mountainous xeroriparian drainages. Using Kaleidoscope Pro, we developed a call‐classifier and processed acoustic data collected in sites also surveyed using traditional human‐observer methods, applying the same spatial and temporal detection criteria to estimate breeding territories for each method. The classifier detected a total of 4,061 true positive calls at 4 sites, had an overall precision score of 0.07, recall score of 0.09, and F‐score (beta = 1) of 0.08, indicating high false positive and false negative classification rates. Our results were, however, consistent with other ARU studies of rare and cryptic species and ARUs estimated occupancy as effectively as human surveys with as little as 2 hours of daily recording. Total detections varied among sites, likely due to differences in cuckoo population densities and the interaction between topography and ARU detection space. Our results suggest that despite performance shortcomings of call‐classifiers, ARUs can be effective for monitoring cuckoos, with potential for providing higher resolution temporal and spatial information on activity and habitat use and may be particularly effective in remote locations where cuckoos often occur.