Ecdysozoa (moulting animals) comprises the protostome Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida and Tardigrada, but our precise understanding of the phylogenetic relationships between these is disputed. Ecdysozoa is an extremely ancient clade that originated in the oceans, and ecdysozoans remain major components of modern marine and terrestrial ecosystems, including the most diverse and abundant of all animal Phyla (Arthropoda and Nematoda respectively). In this thesis, I explore the phylogenetic relationships and divergence times of fossil and extant ecdysozoans in order to address several outstanding issues in the early evolutionary history and palaeobiology of Ecdysozoa, employing data from fossils and molecular sequences. First, the phylogenetic relationships of the eight ecdysozoan phyla was tested using Bayesian models from a molecular matrix containing newly sequenced taxa from Nematomorpha, Priapulida and Tardigrada. Analyses retrieved a monophyletic Scalidophora (Kinorhyncha, Loricifera and Priapulida) which in turn is sister-group to a clade comprising Nematoida (Nematoda and Nematomorpha) and Panarthropoda (Arthropoda, Onychophora and Tardigrada) – this is named Cryptovermes nov. An improved set of fossil calibrations was compiled and used to infer the divergence times of ecdysozoans under a range of alternative parameters. Crown-group Ecdysozoa diverged in the Ediacaran Period between 636 – 578 Ma, at least 23 million years before the oldest potential fossil evidence of ecdysozoans in the late Ediacaran (<556 Ma). Arthropods show more precision and less incongruence with the fossil record compared to other ecdysozoan phyla. Several vermiform (worm-like) fossils from the exceptionally preserved Cambrian Stage 3 Chengjiang Biota of Yunnan Province, south-western China were investigated to address the origin of Ecdysozoa and Panarthropoda in a morphological phylogenetic context. Phylogenetic analyses placed Acosmia maotiania in stem-group Ecdysozoa. Ancestral character state reconstructions revealed the similarities and contrasts between the stem-group ecdysozoan A. maotiania and a reconstruction of the common ancestor of crown-group Ecdysozoa. This reveals that pharyngeal teeth and circumoral armament are likely to be derived traits of the ecdysozoan crown-group, and may have 3 influenced the diversification of crown-group ecdysozoans – perhaps facilitating a change in feeding style (e.g. predation). The cycloneuralians Tabelliscolex hexagonus, Cricocosmia jinningensis and Mafangscolex yunnanensis (=Palaeoscolecidomorpha nov.) share several characters in common with lobopodian panarthropods. This includes paired, seriated ventral trunk structures, corresponding (in T. hexagonus and C. jinningensis) to seriated lateral/dorsolateral trunk sclerites with a net-like microstructure. However, phylogenetic analyses did not retrieve a relationship between palaeoscolecidomorphs and panarthropods, indicating that this style of morphological seriation may have multiple origins within Ecdysozoa. The lobopodian Facivermis yunnanicus is rejected as a model system to understand the acquisition a segmental bodyplan with paired appendages in Panarthropoda. Phylogenies generated here indicate that F. yunnanicus’ worm-like appearance is secondarily adapted from more typical lobopodian ancestors, as a result of adaptation to a specialised tube-dwelling suspension-feeding ecology. Finally, the phylogenetic relationships and divergence times of chelicerate arthropod groups were inferred, and interpreted in the context of arthropod terrestrialization. Phylogenetic analysis of a highly complete matrix of slowly evolving genes supports the monophyly of arachnids. Furthermore, it is parsimonious that the common ancestor of scorpions and other air-breathing arachnids was terrestrial – or at least amphibious – if arachnids are a monophyletic group. Molecular clocks estimate that arachnids diverged in the Cambrian or Early Ordovician, though body fossils of these arthropods are absent until the Silurian which supports the hypothesis of paleontologically cryptic early terrestrial biosphere – mirrored by the molecular and fossil records of myriapods and land plants. Scorpions are the oldest extant terrestrial chelicerate lineage in the fossil record, but is unclear whether the earliest Silurian examples were marine, terrestrial, or even secondarily marine in life.