Paralytic shellfish toxins (PSTs) are highly risk toxins that are produced by various dinoflagellates of the Alexandrium genus in marine environments. Accumulation of these toxins in shellfish provides a serious health risk when consuming contaminated shellfish. High performance liquid chromatography (HPLC) with fluorescence detection is the standard analytical assay for the detection of PST contamination in shellfish samples, but the assay is not straight forward and can only be conducted by a small number of accredited laboratories. Some assays based on capillary electrophoresis (CE) have been reported as alternative to analyze PSTs. In the current work, transient isotachophoresis (tITP) followed by capillary zone electrophoresis (CZE) with capacitively conductivity contactless detection (C⁴D) and UV detection were investigated for the first time for online concentration and analysis of PSTs in shellfish samples. Shellfish typically have a high salt content and in this work the highly mobile sodium ion is used as leading ion for tITP method. By providing the LE through the sample matrix, only terminating electrolyte (TE, L-alanine) needed to be supplied. Analytes stacked by ITP before dissipation of the sodium zone and separation by zone electrophoresis. During electrokinetic TE injection, a hydrodynamic backpressure was also applied from the capillary outlet to increase capillary loadability. Using the tITP-CZE method, the detection limits for the PSTs were decreased to low µg/mL range, gaining a factor of 10 to 30 when compared to CZE without ITP. The method was applied to a mussel sample with good inter-day reproducibility (RSD% <7.5, n = 5) and the calibration curves obtained through standard addition showed a good linear relationship.