"Shadow Over Innsmouth" is one of the classic Lovecraft stories that people forget is about the dangers of race-mixing. African tribes star as villains in quite a few stories, as well. Lovecraft stories are cooler for the genre they started, rather than the stories themselves.
Innsmouth falls under the category of "themes of ancestral heritage and racial purity or impurity" which I was describing. Specifically, Innsmouth is the whole "impurity" by way of interspecies breeding with fish people. Yeah, it's probably symbolism for inter-racial mixing and stuff.
Lovecraft also used racial degeneracy and devolution. Sometimes it was through "mixing" with things such as fish people or humanoid apes from the congos. And sometimes it was through inbreeding of rural hillfolk living in the far away backwaters of New England, descended from colonial people. In other words, white people. White dudes weren't safe from Lovecraft's writing.
I am required to mention, however, that Shadow Over Innsmouth as an anti-miscegenation screed does not make internal logical sense, to the point where I start to doubt that it really is that between the lines like everyone says.
The reason for this is that the end of the tale, after getting the initial shock of discovering he is a Deep One Hybrid, the protagonist ends up accepting his condition and decides that being immortal and living in an undersea paradise actually isn't that bad after all. He then rescues his cousin from the aslyum he's been in for years, since said cousin isn't really crazy, just more informed about the whole fishman thing. The two of them go off to Y'ha-nthlei, and...that's it.
So the message that you shouldn't be a race mixer, even if intended, doesn't really work. "Hey kids, don't sully your blood or else you'll live forever!"