Whitebait comprise a culturally, commercially and recreationally important fishery in New Zealand where post-larvae are netted while returning from their marine phase. In this study, we expanded an historical (1964) sampling program to gain a contemporary understanding of the species composition of the whitebait fishery; 92 rivers were sampled over six months in 2015. Over the entire country, >13 species were found in samples and 84.6% of these were īnanga (Galaxias maculatus). Kōaro (G. brevipinnis) and banded kōkopu (G. fasciatus) were abundant in some rivers and regions at particular times of the year. Buller was the most variable region, spatially and temporally, for species composition; Canterbury was the least variable. Banded kōkopu whitebait migrated one month earlier north of Cook Strait than in the south. There was a positive association between the abundance of kōaro and banded kōkopu in samples and the level of indigenous forest cover in catchments. Compared to samples from 50 years ago, there was a greater proportion of kōaro and banded kōkopu whitebait throughout the country. This spatio-temporal variability requires fishery regulations to be more tailored and flexible if they are to conserve the diversity of life-histories present in the catch and sustain the whitebait fishery.