The inclusion of cover crops into cropping systems may influence soil microbial activity which is crucial to sustained crop production. A study was conducted to measure short term effects of summer and winter cover crops on soil microbial biomass carbon (MBC) in a cucumber-tomato rotation system. The experiment was established in Summer 2002 as a factorial of summer cover crops (planted either as fallow or after harvest of cucumbers) and winter cover crops (planted in September). The design was a split-block with four replications. The main plot factor was summer cover crop and consisted of five treatments; sorghum sudangrass fallow (SGF), cowpea fallow (CPF), sorghum sudangrass after cucumber (SGC), cowpea after cucumber (CPC) and bareground fallow (BGF). The sub-plot factor was winter cover crop and consisted of three treatments including cereal rye (CR), hairy vetch (HV) and bareground (BG). In spring of 2003, soil samples were collected in each treatment at 30 days before (30 DBI), 2 days after (2 DAI) and 30 days after (30 DAI) cover crop incorporation. MBC was measured using the chloroform fumigation-incubation method. Both summer and winter cover crops affected soil microbial activity. MBC in the summer cover crop treatments at 30 DBI was 47.7, 51.4, 49.2, 43.7 and 42.5 μg·g-1 soil for SGF, CPF, SGC, CPC and BGF, respectively. At 30 DAI, 113.1, 88.9, 138.5, 105.6, and 109.3 μg·g-1 soil was obtained in SGF, CPF, SGC, CPC, and BGF plots, respectively. Soil MBC was similar at 2 DAI in the summer cover crop treatments. Among winter treatments MBC was similar at 30 DBI and 30 DAI, but significant at 2 DAI with values of 62.8, 53.3, 59.3 μg·g-1 soil for CR, BG, and HV, respectively.