There isn't one single perfect synonym for "gene pool," but here are some alternatives depending on the context:

General:

* Genetic diversity

* Genetic makeup

* Genetic stock

* Genotype (though this refers to the genetic makeup of an individual)

* Population genetics (a broader concept)

Specific:

* Allele frequency (if referring to the prevalence of specific genes)

* Genome (if referring to the complete set of genes)

* Breeding population (if referring to a group of organisms that interbreed)

* Germ plasm (a less common term referring to the genetic material of a species)

The best alternative depends on the specific meaning you want to convey.