SUMMARY The Swan Islands Transform Fault (SITF) marks the southern boundary of the Cayman Trough and the ocean–continent transition of the North American–Caribbean Plate boundary offshore Honduras. The CAYSEIS experiment acquired a 180-km-long seismic refraction and gravity profile across this transform margin, ∼70 km to the west of the Mid-Cayman Spreading Centre (MCSC). This profile shows the crustal structure across a transform fault system that juxtaposes Mesozoic-age continental crust to the south against the ∼10-Myr-old ultraslow spread oceanic crust to the north. Ocean-bottom seismographs were deployed along-profile, and inverse and forward traveltime modelling, supported by gravity analysis, reveals ∼23-km-thick continental crust that has been thinned over a distance of ∼70 km to ∼10 km-thick at the SITF, juxtaposed against ∼4-km-thick oceanic crust. This thinning is primarily accommodated within the lower crust. Since Moho reflections are not widely observed, the 7.0 km s−1 velocity contour is used to define the Moho along-profile. The apparent lack of reflections to the north of the SITF suggests that the Moho is more likely a transition zone between crust and mantle. Where the profile traverses bathymetric highs in the off-axis oceanic crust, higher P-wave velocity is observed at shallow crustal depths. S-wave arrival modelling also reveals elevated velocities at shallow depths, except for crust adjacent to the SITF that would have occupied the inside corner high of the ridge-transform intersection when on axis. We use a Vp/Vs ratio of 1.9 to mark where lithologies of the lower crust and uppermost mantle may be exhumed, and also to locate the upper-to-lower crustal transition, identify relict oceanic core complexes and regions of magmatically formed crust. An elevated Vp/Vs ratio suggests not only that serpentinized peridotite may be exposed at the seafloor in places, but also that seawater has been able to flow deep into the crust and upper mantle over 20–30-km-wide regions which may explain the lack of a distinct Moho. The SITF has higher velocities at shallower depths than observed in the oceanic crust to the north and, at the seabed, it is a relatively wide feature. However, the velocity–depth model subseabed suggests a fault zone no wider than ∼5–10 km, that is mirrored by a narrow seabed depression ∼7500 m deep. Gravity modelling shows that the SITF is also underlain, at >2 km subseabed, by a ∼20-km-wide region of density >3000 kg m−3 that may reflect a broad region of metamorphism. The residual mantle Bouguer anomaly across the survey region, when compared with the bathymetry, suggests that the transform may also have a component of left-lateral trans-tensional displacement that accounts for its apparently broad seabed appearance, and that the focus of magma supply may currently be displaced to the north of the MCSC segment centre. Our results suggest that Swan Islands margin development caused thinning of the adjacent continental crust, and that the adjacent oceanic crust formed in a cool ridge setting, either as a result of reduced mantle upwelling and/or due to fracture enhanced fluid flow.