Continuous monitoring is essential to understand dynamics of biological communities in response to urbanization, and to provide guidance in landscape planning for conserving urban biodiversity. Arthropods serve this purpose because they are abundant and diverse in urban areas, and relatively easy to collect. Over seven years, in the Central Arizona Phoenix area, arthropod communities in three urban habitat categories were collected and compared to arthropods in natural desert using pitfall traps and non-parametric analyses. First, we tested for differences in arthropod composition, abundances, and diversity across habitats and years. Second, we examined how conclusions about arthropod diversity vary with level of taxonomic resolution. We found that arthropod community composition varied among the four habitats at all taxonomic levels tested. In particular, urban mesic habitats had generally lower diversity than natural desert habitats, although with some exceptions. In contrast, mesic habitats had higher arthropod abundance than all habitats, and fluctuations in abundance were completely independent from changes in precipitation. Taxonomic shortcuts gave overall good impressions of community differences, but finer taxonomic resolutions on certain groups of arthropods revealed distinctly different responses to urbanization (e.g., higher beetle and ant diversity in the urban habitats). Urban areas have great potential for arthropod diversity, but community composition and dynamics are notably different from natural habitats. Institutions, local governments and homeowners can make an impact in arthropod conservation by choice of landscaping, and we recommend that remnants of natural habitats within cities receive further attention in urban planning.