Say you made a tab-delimited text file that looked something like this: sample pop samA 1 samB 2 samC 1 samD 1 samE 3 Where the "sample" column contained the names of your samples exactly as they were in the files with the genotypes (although not necessarily in the same order), and the "pop" column contained the population ID. Say the file is named "mytable.txt". poptable <- read.table("mytable.txt", sep="\t", header=TRUE, row.names=1) PopInfo(mydata) <- poptable[Samples(mydata),"pop"] I like to import tables like this to go with my data, containing geographical or morphological information, colors that I want to use for plotting, etc.