Statistical approach to compare the SNP genotyping data among set of individuals
PCA sounds like a good start to see a rough population structure among your 96 individuals, this step is half a sane thing to do, but also it can give you a hint how many distinct populations there are in your dataset. I have not personally run PCA on SNP data, but it seems that there are quite lot of tutorials online. For instance this one looks  nice.

Once you know how many categories you can expect in your population, you can use Structure to classify individuals to the categories.