The accurate taxonomic identity for the worldwide-distributed invasive ascidian Botryllus schlosseri has not been resolved. Employing molecular tools, primarily mtDNA, previous studies unveiled five divergent clades (A–E), suggesting a complex of five cryptic species. A recent study allocated clades A and E to different species. Here, worldwide B. schlosseri's COI distribution map has been drawn, based on 2927 specimens, elucidating 160 haplotypes (100 singletons). Clade A emerged as the most abundant and globally widespread, while other clades had more limited distributions (primarily B, C). Inter-clade and intra-clade divergences were similar, with no clear barcoding gaps between the clades, illuminating no more than two putative OTUs. Network analyses for the genetic similarities among the clades' haplotypes identified different groups, depending on threshold values and away from the suggested clades' boundaries. Three additional genetic markers (H3, 18S, 28S) disclosed clade A, segregating from other clades and clades D and E strongly integrating. Allorecognition assays between clades resulted in indifference and rejection outcomes, characteristics of the within-species allorecognition repertoire. The question as to whether Botryllus schlosseri is a single species or a species complex is further discussed, leading to the assertion that while it is a widely variable species, there is not enough evidence for its designation as a species complex.