Younger lineage-specific subfamilies exist across the primate radiation, with some subfamilies presently active and others no longer producing new copies or subfamilies. Liu et al. assigned the subfamily designation AluL to elements found in Lemuriformes. Earlier studies have examined aspects of lemur phylogeny using SINEs. Roos, Schmitz, and Zischler used a combination of SINE and mitochondrial markers to reconstruct a phylogeny of the strepsirrhine radiation, while Herke et al. examined relationships among some lemur species as part of a larger study involving the building of an Alu-based key for primate species identification. However, no exclusively Alu-based phylogeny focused on this infraorder has ever been reported. Here, using a combination of computational methods, PCR display methodology, and DNA sequencing, we use 138 Alu insertions specific to the Malagasy strepsirrhine lineage, including 22 loci previously reported by Herke et al. and 17 loci previously reported by Roos, Schmitz, and Zischler. Within the family Cheirogalidae we recovered a strongly supported sister-group relationship between Microcebus and Mirza, with Cheirogaleus recovered as the basal lineage. A total of 19 loci supported the Microcebus-Mirza grouping to the exclusion of Cheirogaleus, which supports the findings of earlier phylogenetic studies. While we were only able to obtain samples from Microcebus murinus for our study, 18 species are currently recognized in Microcebus. The 16 Microcebus-specific loci identified in this study might be useful in future analyses to clarify relationships within this speciose genus. One or more of the Alu elements we identified could certainly be EX 527 clinical trial polymorphic between species in this genus, something we were unable to clarify with only a single species on our panel. In the Indriidae clade we recovered eight loci. Two of these loci, PcC1 and PcC2, were taken from nuclear DNA sequence available via GenBank and are present in all four Indriidae species represented in our dataset. Among the other six loci, three were obtained from the sequencing of ambiguous loci and the remaining three were taken from Roos et al.. Of these six loci, four are present in all four Indriidae species examined in our study. One locus, MmA2c, is specific to Avahi laniger, the eastern wooly lemur. While Alu-based phylogenies are generally reliable, confounding events can occur that result in incongruent tree topologies. In this case it is necessary to resolve relationships between species by DNA sequencing and comparative analysis of the element in question to establish the precise nature of a given locus. An example of a confounding event in the form of a parallel independent insertion is locus MmA20, which appeared to group the Cheirogaleidae with the Indriidae to the exclusion of the other species on our panel. This did not agree with the topology of our tree. Sequencing of this locus in both families demonstrated the presence of a near-parallel independent insertion event, with two Alu elements from independent subfamilies present at nearly the same location in the genome in the two different genera, that is, within the amplicon produced by the primers designed for this locus. MmA20 was then scored as Cheirogaleidae-specific, and MmA20A was scored as Indriidae-specific. Other loci found to contain parallel independent insertions include MmA2, M11, Str67A, and LcC2. Additionally, Ray et al. present an excellent illustrating of potentially confounding Alu insertion events in their study of platyrrhine primate phylogeny.