Connectivity via larval dispersal is an important ingredient in setting effective marine reserve networks. Simple guidance for establishing spacing between individual protected sites can provide reliable rules of thumb to help ensure connectivity. Spacing rules for protected network design are relatively new to marine spatial planning, though so far they have been generically and indiscriminately applied to all types of habitats based on a single range of distance values. Here we address the extent to which such rules capture subtleties associated with dispersal distances varying among species in different regions and habitats. We applied a 50–100 km global spacing rule (SRglob), also recently applied in the California Marine Life Protection Act (MLPA) process and based on available global larval dispersal data, to a previously assessed network in the Gulf of California. Using larval dispersal data for species within this region (SRreg), we associated each species with eight unique habitats (SRhab*) and we evaluated connectivity by means of different spacing rules (SRglob, SRreg and SRhab*) using graph-theory. The existing spacing rule employed by the MLPA process (SRglob) was found to be robust and conservative when applied to the Gulf of California or to its different habitats (i.e., the lower limit for dispersal distance includes the distance for all species in the Gulf). We found that species in different habitats exhibit statistically distinct dispersal profiles. Therefore, some habitats could be evaluated with more relaxed spacing rules (i.e., larger distances), than those proposed by the rules of thumb. Our work identifies a conservation planning trade-off when implementing spacing rules: already proposed rules are robust but at the cost of efficiency. Habitat-specific spacing rules should be considered for more efficient marine conservation planning solutions.