The family Theridiidae is one of the most diverse assemblages of spiders, from both a morphological and ecological point of view. The family includes some of the very few cases of sociality reported in spiders, in addition to bizarre foraging behaviors such as kleptoparasitism and araneophagy, and highly diverse web architecture. Theridiids are one of the seven largest families in the Araneae, with about 2200 species described. However, this species diversity is currently grouped in half the number of genera described for other spider families of similar species richness. Recent cladistic analyses of morphological data have provided an undeniable advance in identifying the closest relatives of the theridiids as well as establishing the family's monophyly. Nevertheless, the comb-footed spiders remain an assemblage of poorly defined genera, among which hypothesized relationships have yet to be examined thoroughly. Providing a robust cladistic structure for the Theridiidae is an essential step towards the clarification of the taxonomy of the group and the interpretation of the evolution of the diverse traits found in the family. Here we present results of a molecular phylogenetic analysis of a broad taxonomic sample of the family (40 taxa in 33 of the 79 currently recognized genera) and representatives of nine additional araneoid families, using approximately 2.5kb corresponding to fragments of three nuclear genes (Histone 3, 18SrDNA, and 28SrDNA) and two mitochondrial genes (16SrDNA and CoI). Several methods for incorporating indel information into the phylogenetic analysis are explored, and partition support for the different clades and sensitivity of the results to different assumptions of the analysis are examined as well. Our results marginally support theridiid monophyly, although the phylogenetic structure of the outgroup is unstable and largely contradicts current phylogenetic hypotheses based on morphological data. Several groups of theridiids receive strong support in most of the analyses: latrodectines, argyrodines, hadrotarsines, a revised version of spintharines and two clades including all theridiids without trace of a colulus and those without colular setae. However, the interrelationships of these clades are sensitive to data perturbations and changes in the analysis assumptions.