Latexes are widely used for industrial applications, including decorative paints, binders for the papermaking industry, and drilling fluids for oil-field applications. In this work, the interest of capillary zone electrophoresis (CE) for the characterization of hydrophobic block copolymer latexes obtained by the conventional emulsion polymerization technique consisting of a core of polystyrene (PS) surrounded by a layer of poly(ethyl acrylate) (PEA) has been investigated. The PEA part of the copolymer can be partially hydrolyzed in poly(acrylic acid) (PAA) leading to PS-PEA-AA water-soluble amphiphilic copolymer having high viscosifying properties. The main purpose of this work was to evaluate the potential of CE for the characterization of the latexes at the different stages of the synthesis (PS core, PS-PEA diblock latex, and hydrolyzed PS-PEA-AA gel). The main analytical issues were to state (i) if there was free PS or PEA homopolymer latexes in the PS-PEA latex sample and (ii) if there was free PS, PEA, PS-PEA latexes, or free PAA chains in the PS-PEA-AA gel. Within this scope, this work describes the optimization of the selectivity of the separation between the different species (PS, PEA particles in the not hydrolyzed diblock latex and PS, PEA, PS-PEA particles as well as the polymer PAA chains in the PS-PEA-AA diblock gel sample obtained by latter latex hydrolysis). For that purpose, several experimental parameters were investigated such as pH and ionic strength of the background electrolyte (BGE) or the concentration of neutral surfactant added in the BGE. A challenging issue was to overcome the high viscosity of the PS-PEA-AA gel. This was resolved by the addition of 10 mM neutral surfactant in the gel sample and in the BGE. Finally, it is demonstrated that, within the detection limits, CE is a suitable analytical tool for controlling and monitoring the syntheses of these latexes and for intrinsically characterizing the distribution in charge density of the final PS-PEA-AA gel at different hydrolysis rates.