Appendicularians are recognized as one of the most abundant mesozooplankton groups in numerous pelagic environments and they play a crucial role in marine ecosystems as they bridge the gap between primary producers and higher trophic levels in the food webs. Zooplankton samples were collected during three spring oceanographic surveys conducted in 2014, 2015, and 2016, in the coastal zone (Staten Island) and oceanic zone (Namuncurá-Banco Burdwood Marine Protected Area). Our study focuses on a comparative analysis of species composition, density, biomass, and maturity stages of appendicularia between these oceanic and coastal regions, which are marked by distinct physical and biological attributes. Two species of appendicularians were found in the study area, Oikopleura fusiformis and Fritillaria borealis, the former being the dominant. Their distribution was different because F. borealis was mainly concentrated in the coastal zone while O. fusiformis was consistently recorded in both zones. Chlorophyll-a concentrations were found to be higher in the coastal zone than in the oceanic zone. These higher concentrations were accompanied by higher densities of O. fusiformis in that area. The surface current velocity seems to reflect the total phytoplankton biomass being higher in the oceanic zone. On the other hand, the temperature for the marine protected area was lower which could be related to the larger sizes of the appendicularians in that zone. Baseline data of the species in protected areas and surrounding areas is essential to contribute to the stakeholders and advise on future changes that translate into regional and global processes.