They can date the rocks but they can also use the measured mutation accumulation rates or a relaxed mutation rate to estimate when two lineages diverged. For most species alive today that’s before about 100,000 years ago with Homo sapiens and Homo neanderthalensis diverging roughly 650,000 years ago accounting for a 0.03% genetic difference between sapiens and Neanderthals. When the percentages are higher the time since they were the same species is also usually higher, save for population bottlenecks and such, so the 1.23% genetic difference between humans and chimpanzees comes out to 6-7 millions years though hybridization may have still been possible 4-4.5 million years ago. For humans and gorillas it’s about 8-10 million years and there hybridization may have still been possible 5-6 million years ago so that, even though humans and chimpanzees were already different lineages, the human lineage could still potentially hybridize with gorillas that diverged first.

The time scales just get larger after that with hominids out to 15-20 million years, apes out to 25-30 million years, monkeys out to about 45 million, and the oldest primate fossils ever found are about 57 million years old pretty close to the 55-56 million years expected based on genomic sequence comparisons. Before that the ancestors of primates looked like the cross between a squirrel and a tree shrew, and tree shrews and then rodents and lagomorphs are the next closest related and their common ancestor lived before the extinction of the non-avian dinosaurs around 66 million years ago.

Eutherians and metatherians diverged roughly around the same time as the first feathered dinosaurs with wings showed up around 160-170 million years ago but both mammals and dinosaurs emerged even earlier yet around 225-250 million years ago. That takes us all the way back to The Great Dying. Before that our synapsid ancestors (the pelycosaurs) were more dominant but after that and until the KT extinction it was the dinosaurs that were the most dominant and once the dinosaurs, the non-avian ones, went extinct, it opened up a lot of niches for the surviving birds, mammals, crocodiles, lizards, and amphibians to fill.

They can’t date all of the fossils directly, so you have a point, but they can date the sediments they are buried in to know when they lived before they died.