Knowing about the spatio-temporal patterns in the structure of ichthyoplankton assemblages allows inferring about the spawning behaviour of adult fishes, understanding the recruitment dynamics, and predicting the potential effects of mid- and long-term changes. Here, we studied the ichthyoplankton assemblages from the San José Gulf (Northern Patagonia, Argentina) and investigated their changes in space and time. To do that, we took monthly samples during two consecutive years, in spring and summer. A total of 2088 larvae were caught; they comprised 36 taxa, from which 14 were identified to species, two to genus, one to family and one to order. There were large differences in the structure of the assemblages between years, coincidently with marked changes in the surface water temperature. The structure of the ichthyoplankton assemblages also showed significant differences between the spring and summer: Helcogrammoides cunninghami, Dules auriga and larvae belonging to the family Engraulidae contributed most to these differences. The species diversity was higher in the colder year than in the warmer one. We discuss the potential role of environmental and oceanographic features on the interannual variability in the early stages of coastal fishes within a small gulf.