The process of speciation is a fascinating area of research in the biological sciences. Development of mathematical and computational models are an important part of developing speciation theory. The Pseudophyte Evolutionary Algorithm PEA is a individual-based population model developed to test hypotheses concerning process of speciation. The individuals pseudophytes are digital "plants." Biologically, they are haploid annuals, each producing pollen and ovules. Pseudophytes are implemented as binary strings representing loci which encoded six traits. Loci were divided into two chromosomes each with three traits. The loci are mapped to a phenotype which determines the behavior of the pseudophyte. The PEA examines the evolution of pre-mating (accepting or rejecting pollen) and postzygotic (offspring inviability) reproductive isolation. Experiments were performed to study the effect of habitat fragmentation, number of loci, method of computing the energy need of a pseudophytes, ovule production, and linkage on the rate at which reproductive isolation evolves. Speciation occurred under low levels of habitat fragmentation, but not high. The effect of moderate habitat fragmentation resulted in faster and more complete reproductive isolation when simulations began with specialist, but speciation did not occur when the initial populations consisted of generalists. Increasing the number of loci tended to delay speciation and result in less between and more within habitat postzygotic isolation. Energy need computation that imposed greater requirements resulted in fewer instances of speciation and less reproductive isolation when it did occur. Linkage experiments revealed complex interaction between the traits.*;*This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Adobe Acrobat; WinZip.