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Echinochrome A (Ech A, <b>1</b>) is one of the main pigments of several sea urchin species and is registered in the Russian pharmacopeia as an active drug substance (Histochrome^®), used in the fields of cardiology and ophthalmology. In this study, Ech A degradation products formed during oxidation by O₂ in air-equilibrated aqueous solutions were identified, isolated, and structurally characterized. An HPLC method coupled with diode-array detection (DAD) and mass spectrometry (MS) was developed and validated to monitor the Ech A degradation process and identify the appearing compounds. Five primary oxidation products were detected and their structures were proposed on the basis of high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) as 7-ethyl-2,2,3,3,5,7,8-heptahydroxy-2,3-dihydro-1,4-naphthoquinone (<b>2</b>), 6-ethyl-5,7,8-trihydroxy-1,2,3,4-tetrahydronaphthalene-1,2,3,4-tetraone (<b>3</b>), 2,3-epoxy-7-ethyl-2,3-dihydro-2,3,5,6,8-pentahydroxy-1,4-naphthoquinone (<b>4</b>), 2,3,4,5,7-pentahydroxy-6-ethylinden-1-one (<b>5</b>), and 2,2,4,5,7-pentahydroxy-6-ethylindane-1,3-dione (<b>6</b>). Three novel oxidation products were isolated, and NMR and HR-ESI-MS methods were used to establish their structures as 4-ethyl-3,5,6-trihydroxy-2-oxalobenzoic acid (<b>7</b>), 4-ethyl-2-formyl-3,5,6-trihydroxybenzoic acid (<b>8</b>), and 4-ethyl-2,3,5-trihydroxybenzoic acid (<b>9</b>). The known compound 3-ethyl-2,5-dihydroxy-1,4-benzoquinone (<b>10</b>) was isolated along with products <b>7</b>–<b>9</b>. Compound <b>7</b> turned out to be unstable; its anhydro derivative <b>11</b> was obtained in two crystal forms, the structure of which was elucidated using X-ray crystallography as 7-ethyl-5,6-dihydroxy-2,3-dioxo-2,3-dihydrobenzofuran-4-carboxylic acid and named echinolactone. The chemical mechanism of Ech A oxidative degradation is proposed. The in silico toxicity of Ech A and its degradation products <b>2</b> and <b>7</b>–<b>10</b> were predicted using the ProTox-II webserver. The predicted median lethal dose (LD₅₀) value for product <b>2</b> was 221 mg/kg, and, for products <b>7</b>–<b>10</b>, it appeared to be much lower (≥2000 mg/kg). For Ech A, the predicted toxicity and mutagenicity differed from our experimental data.