At mid-ocean ridges with fast to intermediate spreading rates, the upper section of oceanic crust is composed of lavas overlying a sheeted dyke complex. These units are formed by dykes intruding into rocks overlying a magma chamber, with lavas erupting at the ocean floor. Seismic reflection data acquired over young oceanic crust commonly image a reflector known as 'layer 2A', which is typically interpreted as defining the geologic boundary between lavas and dykes. An alternative hypothesis is that the reflector is associated with an alteration boundary within the lava unit. Many studies have used mapped variability in layer 2A thickness to make inferences regarding the geology of the oceanic crust, including volcanic construction, dyke intrusion and faulting. However, there has been no link between the geologic and seismological structure of oceanic crust except at a few deep drill holes. Here we show that, although the layer 2A reflector is imaged near the top of the sheeted dyke complex at fast-spreading crust located adjacent to the Hess Deep rift, it is imaged significantly above the sheeted dykes section at intermediate-spreading crust located near the Blanco transform fault. Although the lavas and underlying transition zone thicknesses differ by about a factor of two, the shallow seismic structure is remarkably similar at the two locations. This implies that seismic layer 2A cannot be used reliably to map the boundary between lavas and dykes in young oceanic crust. Instead we argue that the seismic layer 2A reflector corresponds to an alteration boundary that can be located either within the lava section or near the top of the sheeted dyke complex of oceanic crust.