A sequestered germline in Metazoa has been argued to be an obstacle to lateral gene transfer (LGT), though few studies have specifically assessed this claim. Here we test the hypothesis that the origin of a sequestered germline reduced LGT events in Bilateria (i.e. triploblast lineages) as compared to early-diverging Metazoa (i.e. Ctenophora, Cnidaria, Porifera, and Placozoa). We analyze single-gene phylogenies generated with over 900 species, sampled from among Bacteria, Archaea and Eukaryota to identify well-supported interdomain LGTs. We focus on interdomain LGT (i.e. those between prokaryotes and Metazoa) as systematic errors in single gene tree reconstruction create uncertainties for interpreting eukaryote-to-eukaryotes transfers. The breadth of the sampled Metazoa enables us to estimate the timing of LGTs, and to examine the pattern before vs. after the evolution of a sequestered germline. We identified 58 LGTs found only in Metazoa and prokaryotes (i.e. bacteria and/or archaea), and 7 genes transferred from prokaryotes into Metazoa plus one other eukaryotic clade. Our analyses indicate that more interdomain transfers occurred before the development of a sequestered germline, consistent with the hypothesis that this feature is an obstacle to LGT.