New Zealand has the most complete Cenozoic molluscan fossil record in the Southern Hemisphere. In order to understand the true marine faunal history of the region, it is necessary first to identify apparent biodiversity changes that result simply from variations in the quality of the fossil record. The present study uses a range of methods to quantify both long-term, secular changes and short-term patterns of variation in sampling probability for New Zealand Cenozoic shelf molluscs. Overall, about one-third of all once-living Cenozoic species have been sampled, and average per-stage sampling probabilities are between 20% and 50%. Increase in per-stage sampling probability through time reflects the increase in outcrop area and ease of fossil recovery from older to younger stages. Short-term patterns of variation apparently are related to second-order sequence stratigraphic controls of preservation potential. Once the effects of stage duration are eliminated, patterns of stage-to-stage sampling probability reflect enhanced preservation in mid-cycle positions and, perhaps to a lesser extent, secondary post-depositional loss of stratigraphic record above and below sequence boundaries. Although this result mirrors patterns observed in Europe, it is possible that enhanced preservation mid-cycle is relatively more important at active margins, such as New Zealand, whereas secondary loss of record at the sequence boundary is more important at passive margins. Finally, it is worth noting that different methods and data compilations yield rather consistent estimates of short-term variation in sampling probability, lending confidence to the methods and suggesting that the patterns identified are likely to reflect true underlying features of the New Zealand marine fossil record.