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Sea spider fossils (Chelicerata: Pycnogonida) are restricted to eleven species sparsely distributed from the Silurian to the Jurassic. Their morphology and relationships to extant pycnogonids are poorly understood. To improve their description, nest them in the chelicerate phylogeny and decipher the timing of Pycnogonida’s evolution, we conducted a comprehensive reinvestigation of the sea spider fossil record. We studied approximately 60 fossils, published or new, from the KonservatLagerstätten of Herefordshire, UK (Silurian), the Hunsrück Slate, Germany (Devonian), La Voulte-sur-Rhône, France and Solnhofen, Germany (Jurassic). Using X-ray microtomography, Reflectance Transformation Imaging, serial grinding and microtopography, we illustrate the past diversities of Pycnogonida. We show that while Palaeozoic fossils exhibit a stunning diversity of forms and adaptations unmatched in extant species, Mesozoic fossils share the same body plan as extant sea spiders, suggesting they belong to the crown-group Pycnogonida, i.e. Pantopoda. By performing the first total-evidence phylogeny of Chelicerata including the eleven sea spider fossil species, we further support our taxonomic interpretations. We demonstrate that Mesozoic fossils are nested within extant families or superfamilies, while Palaeozoic species belong to the stem-group Pycnogonida. Finally, we date the phylogeny of Pycnogonida using both node-dating and tip-dating strategies and estimate the divergence time of major Pycnogonida lineages.