[r] Simplest way to do grouped barplot

There are several ways to do plots in R; lattice is one of them, and always a reasonable solution, +1 to @agstudy. If you want to do this in base graphics, you could try the following:

Reasonstats <- read.table(text="Category         Reason  Species
                                 Decline        Genuine       24
                                Improved        Genuine       16
                                Improved  Misclassified       85
                                 Decline  Misclassified       41
                                 Decline      Taxonomic        2
                                Improved      Taxonomic        7
                                 Decline        Unclear       41
                                Improved        Unclear      117", header=T)

ReasonstatsDec <- Reasonstats[which(Reasonstats$Category=="Decline"),]
ReasonstatsImp <- Reasonstats[which(Reasonstats$Category=="Improved"),]
Reasonstats3   <- cbind(ReasonstatsImp[,3], ReasonstatsDec[,3])
colnames(Reasonstats3) <- c("Improved", "Decline")
rownames(Reasonstats3) <- ReasonstatsImp$Reason

windows()
  barplot(t(Reasonstats3), beside=TRUE, ylab="number of species", 
          cex.names=0.8, las=2, ylim=c(0,120), col=c("darkblue","red"))
  box(bty="l")

enter image description here

Here's what I did: I created a matrix with two columns (because your data were in columns) where the columns were the species counts for Decline and for Improved. Then I made those categories the column names. I also made the Reasons the row names. The barplot() function can operate over this matrix, but wants the data in rows rather than columns, so I fed it a transposed version of the matrix. Lastly, I deleted some of your arguments to your barplot() function call that were no longer needed. In other words, the problem was that your data weren't set up the way barplot() wants for your intended output.