Southeast Asia is arguably the most tectonically active region on the planet, fuelled to a large extent by nearly 10,000 km of ongoing subduction on its western, southern and eastern flanks that accommodates the northward motion of the Indo-Australian plate and westward motion of the Philippine Sea plate. It has hosted one of the largest earthquakes ever recorded (Mw 9.2 Sumatra-Andaman earthquake in 2004) and perhaps the most famous volcanic eruption in history (Krakatoa eruption of 1883), which profoundly affected the Earth's climate. While the western Pacific margin and Indonesian archipelago along the Sunda and Banda arcs have been well studied, the same is not true of the interior region of Southeast Asia, which includes Borneo and Sulawesi. Borneo is the 3rd largest island in the world and lies on the eastern margin of Sundaland, the continental core of Southeast Asia, but its intraplate setting means that it has no active volcanoes and little in the way of seismicity. By contrast, the adjacent island of Sulawesi features active subduction and a network of continental transform faults that give rise to high levels of earthquake activity. How this central region of southeast Asia was formed, and the tectonic relationship between Borneo and Sulawesi, is still poorly understood. The goal of this thesis is to exploit passive seismic data recorded by temporary and permanent seismic networks to image the first order crustal structure of both Borneo and Sulawesi. This will provide fresh insight into their deep structure, provenance and tectonic evolution, and how they have been impacted by recent events (e.g. opening of the South China Sea) that have clearly left their mark on surrounding regions. The passive seismic data used in this dissertation is in the form of teleseismic body wave arrivals, which interact with upper mantle and crustal structure before being recorded by stations on the surface. I utilise both receiver function analysis (RFA) and virtual deep seismic sounding (VDSS) to extract information from mode converted and reflected phases to constrain seismic properties including Moho depth, V_S and V_P 〖/V〗_S. In the case of RFA, H-k stacking, migration and inversion are separately applied, with the ensemble of results producing robust estimates of crustal thickness in particular. The primary strength of VDSS is its ability to constrain Moho depth using relative few sources, even in the presence of significant crustal complexity (e.g. thick sedimentary sequences); I therefore find this to be a particularly useful technique in some regions, such as northern Borneo, where RFA produces equivocal results due to strongly heterogeneous crustal structure. One of the main outcomes of this thesis is a new detailed map of Moho depth variations beneath northern Borneo from the application of VDSS to data from an array of 65 temporary and permanent broadband seismometers. This is the most recently active part of Borneo, having experienced at least two phases of subduction in the Miocene. Moho depths vary between ~45 km beneath the Crocker Range to less than 25 km beneath the central interior, consistent with the presence of a thick crustal root transitioning to an area of relatively thin crust that extends NE into the Sulu Sea. These results support a model of subduction polarity reversal (SPR) in Borneo, in which opening of the South China Sea led to SE-directed subduction of the proto-South China Sea beneath Northern Borneo, followed by continent-continent collision, which formed the Crocker Range, supported by a thicker crust. This was followed by subduction termination and the initiation of Celebes Sea subduction beneath northern Borneo of opposite polarity. Roll-back of the Celebes Sea slab resulted in the opening of the Sulu Sea, which extended into the interior of northern Borneo and caused localised crustal thinning, but did not proceed to rifting. In addition to the detailed study of northern Borneo, I also investigated Borneo in its entirety, albeit at a much lower resolution owing to the more limited data coverage at this scale. The primary tool in this case was RFA, which was used on data from 28 broadband stations distributed throughout Sarawak and Kalimantan, as well as a subset of stations from northern Borneo. VDSS was also applied to data recorded at a number of sites where RFA was not able to produce a well constrained Moho. The results show that on a broad scale, northern Borneo features the thickest crust, with the vast majority of Borneo having crust that is less than 35 km thick, despite the interior mountain range having an average elevation in excess of 1000 m. Some of the thinnest crust (~25 km) occurs beneath a Mesozoic accretionary complex in western Borneo, which is thought to mark the location of a previous subduction zone and crustal extension related to slab rollback. In Southwest Borneo, the Schwaner mountains are underlain by elevated V_P 〖/V〗_S, which are juxtaposed against lower Vp/Vs of the Kuching Zone. Thicker crust (~40 km) in southeast Borneo approximately overlays the Meratus Suture, and may be related to the docking of the East Java-West Sulawesi and Southwest Borneo blocks, which have East Gondwana provenance. The investigation of the crustal structure of Sulawesi made use of data from 23 permanent network stations and 18 temporary stations, with receiver function analysis applied to constrain the bulk crustal properties of Sulawesi. Crustal thickness ranges between about 20 km and 40 km, with the thinnest and thickest crust juxtaposed across the Palu-Koro fault, a > 500 km long sinistral strike slip fault in central Sulawesi. This fault - which produced an Mw 7.5 earthquake in 2015 that also unleashed a destructive tsunami - accommodates some 4 cm/yr of left-lateral motion along with clockwise motion of the North Arm of Sulawesi. Thinner crust along the western part of the North Arm of Sulawesi is likely related to roll-back along the North Sulawesi trench, while thicker crust to the east may be due to opposed subduction of the Celebes Sea and Molucca Sea straddling the land mass. The relatively simple crustal seismic models of Borneo and Sulawesi produced in this dissertation represent a solid first step towards understanding their tectonic assemblage and geological architecture. Future work might involve bringing in other datasets to aid with interpretation, such as gravity, magnetic, heat flow, geochronology, petrology etc., and using the new seismic models to help answer first order questions, such as the mismatch between predicted and observed dynamic topography in Borneo in particular. Incorporating data from a recent OBS deployment in the southern Celebes Sea and Makassar Strait may significantly improve our ability to connect the seismic structure of Borneo and Sulawesi, although it remains to be seen whether the data coverage and quality will be sufficient to substantially change the current picture.