The nucleotide sequences of two Sida-infecting geminiviruses from Honduras were determined. The symptoms of both viruses are identical in Sida rhombifolia but different in Nicotiana benthamiana. An additional symptom of one virus was yellow vein clearing on infected N. benthamiana leaves. Both Sida golden mosaic viruses (SiGMV-Ho and SiGMV-Ho(yv)) have bipartite genomes (DNAs A and B). From the SiGMV-Ho(yv)-infected S. rhombifolia plant two different DNA B molecules were isolated and cloned. They differ in length by 24 nucleotides [SiGMV-Ho(yv) B1 (2593 nt) and B2 (2569 nt)] and at eight nucleotide positions. Both proteins encoded by DNA B (BV1 and BC1) are affected by these substitutions. Computer analysis shows that the bipartite genomes resemble those of other whitefly-transmitted geminiviruses. From homology analyses we conclude that both viruses are closely related but distinct. Comparison with a Sida-infecting virus from Costa Rica (SiGMV-Co) showed that the two viruses from Honduras are more similar to each other than either of them are to SiGMV-Co. Exchange of SiGMV-Ho and SiGMV-Ho(yv) genomic components resulted in viable pseudorecombinant viruses. SiGMV-Ho DNA A was able to produce a viable pseudorecombinant with SiGMV-Co DNA B while the reciprocal exchange was not infectious in N. benthamiana. SiGMV-Ho(yv) DNA A and SiGMV-Co DNA B produced a viable pseudorecombinant virus whereas only pseudorecombination of SiGMV-Co DNA A with SiGMV-Ho(yv) DNA B2, and not with DNA B1, was infectious in N. benthamiana.