You mean how they were able to identify....Even after 900 more years of occasional intermarriage between Jews and Christians it was still possible to identify a Jew by looks alone. Just ask any Nazi, or anyone who agreed with them on this question. Nazi propaganda is full of claims that "Jews look funny/odd/different" or "You can tell he's Jewish just by looking at him." These claims fell on receptive ears. I doubt the Nazis would have made these claims if there was no credibility to the statement that Jews did look different than non-Jews. If this claim wasn't credible, there were so many other claims the Nazis could have made instead.
Even if there were no outward biological differences, there could be cultural differences - choices in fashion, hair style, name choices, etc.