While photo-identification is an effective tool to monitor individuals in wild populations, it has limitations. Specifically, it cannot be applied to very young animals before their identifying features have stabilized or to dead, decomposed animals. These shortfalls leave gaps in our understanding of survival, parentage, age structure, physical development, and behavioral variability. Here we report on 13 case studies of North Atlantic right whale, Eubalaena glacialis, calves that required genetics to track their life history data. These case studies revealed unexpected variations in mother–calf associations and separation times, as well as calf physical development. Prior to this study, calves were assumed to have died if their mothers were always alone on the feeding ground in the calf’s birth year. Using genetics and photo-identification, four such calves were discovered to be alive; two of the four possibly weaned earlier than expected at 7.5–8.0 months. To put these early separations in context, photo-identification data were queried and revealed that mothers and calves are seen apart from each other on the feeding grounds in 10–40% of all spring/summer sightings; previously, there were no published data on how often pairs are seen apart in the calf’s birth year. Two dead whales initially logged as calves of the year were discovered to be juveniles, thus allowing skewed survival estimates for calves of the year to be corrected. Genetically sampling animals early in their lives before they disperse or separate from their mothers provides an important means of individual identification at a time when photo-identification is not reliable.