Serpentinites and serpentinized mantle peridotites with various tectonic origins occur in the Franciscan Complex of the Northern California Cordillera, USA. Boron isotopes of serpentinites differentiate with fluid-mediated processes, and have great potential for key geologic markers in convergent margins. To understand boron isotope behavior within the Franciscan subduction zone system, we apply a newly developed ablation volume correction (AVC) method for in-situ isotope/elemental analyses using a laser-ablation multiple collector inductively-coupled-plasma mass spectrometry (LA-MC-ICPMS) on seventeen different Franciscan serpentinites (sensu lato) collected from eight separate areas. Boron abundances and isotope compositions of the studied serpentinites show large variations B = 1.6–239 µg·g−1, δ11B = −12.0 to +24.4‰, which allow to discriminate the serpentinites into two groups: (1) a lighter δ11B of –12.0 to +8.8 ‰ with a lesser B < ~56 μg·g−1 and (2) a heavier δ11B of +7.2 to +24.4% with a greater B ~34–239 µg·g−1. These groups lithologically correspond to the presence or absence of associated blueschist-facies metamorphic rocks, respectively. The blueschist-bearing and/or blueschist-associated serpentinites might have been affected by a deep forearc slab fluids in the depth of > ~2 GPa. Preferential partitioning of 11B into fluids released from the subducted slab at shallow leaves lighter δ11B in the slab resulting in lighter δ11B in the deep slab fluids. In contrast, the blueschist-absent serpentinites with heavier δ11B may have formed at a shallow environment where shallow slab or hydrothermal fluids with heavier 11B were present. Lesser versus greater amounts of B in the deep versus shallow serpentinites are also consistent with the dehydration profile of B from a slab. Our results show the versatility of B isotopes and composition for identification of the origin of serpentinite in Pacific-type orogenic belts.