Thermoplastic composite structures based on continuous carbon fiber reinforcements are gaining importance in many industrial applications. These comprise basic technical functions as well as high performance applications in the aerospace sector. Welding techniques are applicable for composites based on thermoplastic matrix materials in contrast to thermoset systems. In this context, welding steps are not limited to the joining of carbon fiber reinforced plastic (CFRP) parts among themselves, but extend to the connection of various components, consisting of unreinforced and glass fiber reinforced thermoplastics to CFRP components. In this work, a laser transmission welding process is evaluated with respect to the influence of the carbon fiber reinforcement within the laser absorbing part as well as the glass fiber reinforcement within the laser transparent part on the weld seam formation. Thermoplastic base material nylon (PA 6.6) and polyphenylene sulfide (PPS) are used. By applying two different strategies, contour and quasi-simultaneous welding, the influence of continuous fiber reinforced composites on the welding process is studied. Significant differences to the process characteristics known from the joining of unreinforced thermoplastics emerge from the fiber reinforcement inducing high thermal conductivity and fluctuating absorption properties for the laser wavelength, resulting in an essentially altered plastification performance which is directly mirrored in the inhomogeneous formation of the weld seam structure.