Agarose gel electrophoresis (AGE) has been widely implemented throughout veterinary medicine and for analysis of plasma proteins of avian and reptile species. Capillary zone electrophoresis (CZE) is becoming a standard method in human clinical pathology laboratories but has not widely been used for the analysis of animal samples. The objective of the present study was to compare protein fractions derived from AGE and CZE methods using plasma from the green turtle (Chelonia mydas). Plasma samples were analyzed by AGE and CZE per manufacturer guidelines. The methods were assessed by CV analysis, Spearman's correlation, Passing-Bablok regression, and Bland Altman plots. CZE consistently resolved more fractions than AGE with three fractions observed in the prealbumin migrating region versus one for AGE and two fractions in the γ globulin region versus one for AGE. Compared with AGE, CZE showed a lower CV in intra-assay tests (1.0–4.9% vs 2.0–28.3%) and a lower or overlapping CV in interassay tests (1.0–10.6 vs 2.3–22.0). The prealbumin, α2 globulin, and β globulin fractions correlated the least between the methods (for all three fractions: r_s ≤ 0.28, P > 0.21). Moderate, significant correlations between AGE and CZE methods were observed for albumin (r_s = 0.78, P < 0.0001) and γ globulins (r_s = 0.78, P < 0.0001). CZE has a higher precision and ease of use over AGE and offers the opportunity to resolve additional protein fractions. This will necessitate the development of new conventions in placement of fraction delimits, definition of species-specific reference intervals, and evaluation of clinical utility in abnormal turtles.