South American sea lions (Otaria byronia) and Peruvian fur seals (Arctocephalus australis) are sympatric species inhabiting the coastal Peruvian marine ecosystem. Declining abundance has prompted population health monitoring programs, including temporal monitoring of blood parameters. Several methodologies exist to determine total leukocyte count, yet no studies have evaluated agreement between methods in pinnipeds. We assessed agreement between total leukocyte counts determined by blood film estimate, Leuko-TIC, HemoCue, and UNOPETTE methods by using archival results from pinnipeds at Punta San Juan, Peru. Blood film estimates were prospectively performed, and resulting data were compared with retrospective leukocyte counts obtained from both species between 2009 and 2019 by using the other methodologies. Agreement in hematologic counts between methods was evaluated using Passing-Bablok regression and Bland-Altman plots (α=0.05). In total, 295 individuals (201 A. australis and 94 O. byronia) were included in the analysis. The blood film estimate method resulted in the highest leukocyte values (P<0.0001). Leuko-TIC counts were significantly higher than HemoCue counts (P<0.0001). Constant and proportional error was present in the agreement between the blood film estimate method and the other methods. Given the variation demonstrated between the different methodologies, additional research is needed to further evaluate agreement between these methodologies. The results underscore the importance of maintaining consistency in leukocyte count methodology for monitoring trends in population health over time. Method consistency may be the more important clinical consideration for assessing changes in leucocyte count over time and avoiding apparent changes depending on the methodology used.