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Abstract The ratio of boron to calcium (B/Ca) in a subset of foraminifera has been shown to covary with seawater carbonate chemistry, making this geochemical signature a promising proxy for carbon cycle science. Some studies suggest complications with the B/Ca proxy in photosymbiont‐bearing planktonic foraminifera, while relatively few studies have investigated B/Ca in species that lack large dinoflagellate symbionts. For the first time, we use a sediment trap time series to evaluate B/Ca of subtropical and subpolar planktonic foraminifera species that are asymbiotic (Globigerina bulloidesandNeogloboquadrina incompta) and a species that hosts small intrashell photosymbionts (Neogloboquadrina dutertrei). We find that B/Ca measurements across size fractions indicate overall little to no size‐dependent uptake of boron that has previously been reported in some symbiont‐bearing foraminifera.Neogloboquadrina incomptaandN.dutertreiB/Ca are strongly correlated with calcite saturation, pH, and carbonate ion concentration, which is in good agreement with the limited number of published core top results. WhileG.bulloidesB/Ca trends with seasonal fluctuations in carbonate chemistry, during discrete periods considerable B/Ca offsets occur when a crypticG.bulloidesspecies is known to be seasonally present within the region. We confirm presence and significant B/Ca offset between cryptic species by individual LA‐ICP‐MS analyses. This finding calls into question the use of traditional morphological classification to lump what might be genetically distinct species for geochemical analyses. Our overall results highlight the utility ofG.bulloides,N.incompta, andN.dutertreiB/Ca while bringing to light new considerations regarding divergent geochemistry of cryptic species.