Identifying population differentiation at specific sites across the genome in non-model organisms has been difficult historically. Here, I present the results of a combination of approaches to convert the non-model organism Eulimnadia texana (the clam shrimp) into a practical system for genomics, and show evidence of differentiation of genomic sites apparently due to adaptive evolution. Clam shrimp are attractive for genetics because of their small genome size (150Mb), large populations, short generations (~3 weeks), and their ability to lay eggs that can remain in diapause for decades without loss of viability. I generated a whole genome, hybrid de novo assembly of the clam shrimp genome (assembly N50: 18Mb) using a combination of Illumina short read genomic data and PacBio long read data. I used Illumina RNA sequencing of both male and hermaphrodite clam shrimp in order to annotate the genome, then compared the genome to those of Drosophila melanogaster and the closest sequenced relative of the clam shrimp, the water flea Daphnia pulex, and used differential gene expression analysis to identify genes that significantly differ in expression between males and hermaphrodites. I generated allele frequency estimates from pooled sequencing data from 11 separate wild populations of clam shrimp and estimated average linkage disequilibrium, FST, and other classic population genetics statistics. Both bayesian methods and FST analysis of populations revealed candidate selection sites. I correlated these with a variety of environmental factors, including presence of predators, vernal pool dimensions, and ratio of clam shrimp males to hermaphrodites. I identified multiple sites that appear significantly diverged and that have annotated genes that may be under adaptive evolution in these populations.